# HG changeset patch # User jankanis # Date 1400507034 14400 # Node ID a54279222d84c557a04de1658629fc73a141d570 Imported from capsule None diff -r 000000000000 -r a54279222d84 NCBI Blast reference example.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NCBI Blast reference example.html Mon May 19 09:43:54 2014 -0400 @@ -0,0 +1,2071 @@ + + + + + + + + + + + + + + + +NCBI Blast:Nucleotide Sequence (16 letters) + + + + + + + + + + + + + + +
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+ + +
  • Your search parameters were adjusted to search for a short input sequence.

+ Edit and Resubmit + +[Sign in above to save your search strategy] + + + +How to read this page +Blast report description + +
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+ +
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+
+ +
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+

Nucleotide Sequence (16 letters)

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+ + +
+ +
+
+
+
+
RID
+
+PHWP1JNZ014 (Expires on 05-07 22:33 pm) +
+
+
+
+
Query ID
+ +
lcl|59987
+
Description
+
None
+
Molecule type
+
nucleic acid
+
Query Length
+
16
+
+
+ +
+
+
+
Database Name
+
pdb
+
Description
+
PDB nucleotide database
+
Program
+
BLASTN 2.2.29+
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+ +
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+ +
+

+ +Alignments + + +

+ +
+
+
+
+
+ + + +GenBankGraphics + + + +Next +Previous +Descriptions + +
+
+
+
+Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Classic Post- Translocation State (post1, 50s Subunit) +
pdb|3J5A|A29034
+
+
+
+ +
+ + + + + + + + + + + + + +
Alignment statistics for match #1
ScoreExpectIdentitiesGapsStrandFrame
32.2 bits(16)8e-04()16/16(100%)0/16(0%)Plus/Plus
+ +
+
+
Query  1    CGTCCGTCGTGAAGAG  16
+            ||||||||||||||||
+Sbjct  961  CGTCCGTCGTGAAGAG  976
+
+
+
+
+
+ + + + + + + + + + + + + +
Alignment statistics for match #2
ScoreExpectIdentitiesGapsStrandFrame
16.4 bits(8) 47()8/8(100%)0/8(0%)Plus/Plus
+ +
+
+
Query  5     CGTCGTGA  12
+             ||||||||
+Sbjct  2591  CGTCGTGA  2598
+
+
+
+
+
+ + + + + + + + + + + + + +
Alignment statistics for match #3
ScoreExpectIdentitiesGapsStrandFrame
14.4 bits(7) 186()7/7(100%)0/7(0%)Plus/Plus
+ +
+
+
Query  7    TCGTGAA  13
+            |||||||
+Sbjct  839  TCGTGAA  845
+
+
+
+
+
+ + + + + + + + + + + + + +
Alignment statistics for match #4
ScoreExpectIdentitiesGapsStrandFrame
14.4 bits(7) 186()7/7(100%)0/7(0%)Plus/Plus
+ +
+
+
Query  9     GTGAAGA  15
+             |||||||
+Sbjct  2027  GTGAAGA  2033
+
+
+
+
+
+
+
+ + + +GenBankGraphics + + + +Next +Previous +Descriptions + +
+
+
+
+Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Hybrid Pre- Translocation State (pre5b, 50s Subunit) +
pdb|3J58|A29034
+
+
+
+ +
+ + + + + + + + + + + + + +
Alignment statistics for match #1
ScoreExpectIdentitiesGapsStrandFrame
32.2 bits(16)8e-04()16/16(100%)0/16(0%)Plus/Plus
+ +
+
+
Query  1    CGTCCGTCGTGAAGAG  16
+            ||||||||||||||||
+Sbjct  961  CGTCCGTCGTGAAGAG  976
+
+
+
+
+
+ + + + + + + + + + + + + +
Alignment statistics for match #2
ScoreExpectIdentitiesGapsStrandFrame
16.4 bits(8) 47()8/8(100%)0/8(0%)Plus/Plus
+ +
+
+
Query  5     CGTCGTGA  12
+             ||||||||
+Sbjct  2591  CGTCGTGA  2598
+
+
+
+
+
+ + + + + + + + + + + + + +
Alignment statistics for match #3
ScoreExpectIdentitiesGapsStrandFrame
14.4 bits(7) 186()7/7(100%)0/7(0%)Plus/Plus
+ +
+
+
Query  7    TCGTGAA  13
+            |||||||
+Sbjct  839  TCGTGAA  845
+
+
+
+
+
+ + + + + + + + + + + + + +
Alignment statistics for match #4
ScoreExpectIdentitiesGapsStrandFrame
14.4 bits(7) 186()7/7(100%)0/7(0%)Plus/Plus
+ +
+
+
Query  9     GTGAAGA  15
+             |||||||
+Sbjct  2027  GTGAAGA  2033
+
+
+
+
+
+
+
+ + + +GenBankGraphics + + + +Next +Previous +Descriptions + +
+
+
+
+Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Hybrid Pre- Translocation State (pre5a, 50s Subunit) +
pdb|3J56|A29034
+
+
+
+ +
+ + + + + + + + + + + + + +
Alignment statistics for match #1
ScoreExpectIdentitiesGapsStrandFrame
32.2 bits(16)8e-04()16/16(100%)0/16(0%)Plus/Plus
+ +
+
+
Query  1    CGTCCGTCGTGAAGAG  16
+            ||||||||||||||||
+Sbjct  961  CGTCCGTCGTGAAGAG  976
+
+
+
+
+
+ + + + + + + + + + + + + +
Alignment statistics for match #2
ScoreExpectIdentitiesGapsStrandFrame
16.4 bits(8) 47()8/8(100%)0/8(0%)Plus/Plus
+ +
+
+
Query  5     CGTCGTGA  12
+             ||||||||
+Sbjct  2591  CGTCGTGA  2598
+
+
+
+
+
+ + + + + + + + + + + + + +
Alignment statistics for match #3
ScoreExpectIdentitiesGapsStrandFrame
14.4 bits(7) 186()7/7(100%)0/7(0%)Plus/Plus
+ +
+
+
Query  7    TCGTGAA  13
+            |||||||
+Sbjct  839  TCGTGAA  845
+
+
+
+
+
+ + + + + + + + + + + + + +
Alignment statistics for match #4
ScoreExpectIdentitiesGapsStrandFrame
14.4 bits(7) 186()7/7(100%)0/7(0%)Plus/Plus
+ +
+
+
Query  9     GTGAAGA  15
+             |||||||
+Sbjct  2027  GTGAAGA  2033
+
+
+
+
+
+
+
+ + + +GenBankGraphics + + + +Next +Previous +Descriptions + +
+
+
+
+Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Hybrid Pre- Translocation State (pre4, 50s Subunit) +
pdb|3J54|A29034
+
+
+
+ +
+ + + + + + + + + + + + + +
Alignment statistics for match #1
ScoreExpectIdentitiesGapsStrandFrame
32.2 bits(16)8e-04()16/16(100%)0/16(0%)Plus/Plus
+ +
+
+
Query  1    CGTCCGTCGTGAAGAG  16
+            ||||||||||||||||
+Sbjct  961  CGTCCGTCGTGAAGAG  976
+
+
+
+
+
+ + + + + + + + + + + + + +
Alignment statistics for match #2
ScoreExpectIdentitiesGapsStrandFrame
16.4 bits(8) 47()8/8(100%)0/8(0%)Plus/Plus
+ +
+
+
Query  5     CGTCGTGA  12
+             ||||||||
+Sbjct  2591  CGTCGTGA  2598
+
+
+
+
+
+ + + + + + + + + + + + + +
Alignment statistics for match #3
ScoreExpectIdentitiesGapsStrandFrame
14.4 bits(7) 186()7/7(100%)0/7(0%)Plus/Plus
+ +
+
+
Query  7    TCGTGAA  13
+            |||||||
+Sbjct  839  TCGTGAA  845
+
+
+
+
+
+ + + + + + + + + + + + + +
Alignment statistics for match #4
ScoreExpectIdentitiesGapsStrandFrame
14.4 bits(7) 186()7/7(100%)0/7(0%)Plus/Plus
+ +
+
+
Query  9     GTGAAGA  15
+             |||||||
+Sbjct  2027  GTGAAGA  2033
+
+
+
+
+
+
+
+ + + +GenBankGraphics + + + +Next +Previous +Descriptions + +
+
+
+
+Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Classic Pre- Translocation State (pre1a, 50s Subunit) +
pdb|3J52|A29034
+
+
+
+ +
+ + + + + + + + + + + + + +
Alignment statistics for match #1
ScoreExpectIdentitiesGapsStrandFrame
32.2 bits(16)8e-04()16/16(100%)0/16(0%)Plus/Plus
+ +
+
+
Query  1    CGTCCGTCGTGAAGAG  16
+            ||||||||||||||||
+Sbjct  961  CGTCCGTCGTGAAGAG  976
+
+
+
+
+
+ + + + + + + + + + + + + +
Alignment statistics for match #2
ScoreExpectIdentitiesGapsStrandFrame
16.4 bits(8) 47()8/8(100%)0/8(0%)Plus/Plus
+ +
+
+
Query  5     CGTCGTGA  12
+             ||||||||
+Sbjct  2591  CGTCGTGA  2598
+
+
+
+
+
+ + + + + + + + + + + + + +
Alignment statistics for match #3
ScoreExpectIdentitiesGapsStrandFrame
14.4 bits(7) 186()7/7(100%)0/7(0%)Plus/Plus
+ +
+
+
Query  7    TCGTGAA  13
+            |||||||
+Sbjct  839  TCGTGAA  845
+
+
+
+
+
+ + + + + + + + + + + + + +
Alignment statistics for match #4
ScoreExpectIdentitiesGapsStrandFrame
14.4 bits(7) 186()7/7(100%)0/7(0%)Plus/Plus
+ +
+
+
Query  9     GTGAAGA  15
+             |||||||
+Sbjct  2027  GTGAAGA  2033
+
+
+
+
+
+
+
+ +
+
+
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+ +
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PreferencesTurn off
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words = $("qorganism").value.split(" (taxid"); + $("qorganism").value = words[0]; +} + + +/* JS Common to all BLAST pages */ + + +function setResultsTarget() +{ + //var newWin = $("newwin"); + var newWin = this; + var searchFrm = $(newWin.getAttribute("form")); + if(newWin && newWin.checked == true) { + if(newWin.getAttribute("winType") == "random") { + searchFrm.target = "Blast_Results_for_" + Math.floor(Math.pow(10,10) *Math.random()); + } + else { + searchFrm.target = $("resPageTarget").value; + } + } + else { + searchFrm.target = ""; + } +} + +function diffFromDefault(elem) +{ + var currentVal = ""; + var ret = 0; + + if (!(elem)) return; + var defVal = elem.getAttribute("defVal"); //Default value + var elShowDiff = utils.getParent(elem); + if(!elem.type) {//div element for example + //Check if parent elem has "hide" class + if(utils.hasClass(utils.getParent(elem), "hide")) { + currentVal = "hide"; + } + else { + currentVal = "show"; + } + elShowDiff = elem; + } + else if(elem.type == "select-one") { + if(elem[elem.selectedIndex].value) currentVal = elem[elem.selectedIndex].value; + //If Default value is not specified - the first one in the selection list is the default + if (!defVal && elem[0].value) defVal = elem[0].value; + } + else if(elem.type == "select-multiple") { + currentVal = "";//for now + } + else if(elem.type == "checkbox") { + //alert("defVal1=" + elem.id + " " + defVal); + //var defVal = elem.defVal; //Default value + //alert("defVal2=" + defVal); + if(elem.checked == true) currentVal = "checked" + else currentVal = "unchecked"; + } + else { + currentVal = elem.value; + } + + + var numdiff = parseInt($("NUM_DIFFS").value,10); + var optsNumDiff = parseInt($("NUM_OPTS_DIFFS").value,10); + if(defVal != currentVal) { + if(!utils.hasClass(elShowDiff, "nondef")) { + utils.addClass(elShowDiff, "nondef"); + numdiff++; + if(utils.hasClass(elem,"opts")) optsNumDiff++; + } + ret = 1; + } + else { + if(utils.hasClass(elShowDiff, "nondef")) { + utils.removeClass(elShowDiff, "nondef"); + //alert("noDiff-" + elem.id); + if(numdiff != 0) numdiff--; + if(utils.hasClass(elem,"opts")) optsNumDiff--; + } + ret=0; + } + $("NUM_DIFFS").value = numdiff; + $("NUM_OPTS_DIFFS").value = optsNumDiff; + if(numdiff > 0) { + $("diffMes").style.display = "inline"; + } + else { + $("diffMes").style.display = "none"; + } + //alert(elem.id + " " + $("NUM_DIFFS").value); + return ret; +} + +function setDefalValue(elem) +{ + var currentVal; + var defVal = elem.getAttribute("defVal"); //Default value + if(elem.type == "select-one") { + //If Default value is not specified - the first one in the selection list is the default + if(!defVal) defVal = elem[0].value; + for(j=0; j < elem.options.length; j++) { + if(elem.options[j].value == defVal) { + elem.options[j].selected = true; + break; + } + } + } + else if(elem.type == "checkbox" || elem.type == "radio") { + if(!defVal) defVal = "checked"; + if(defVal == "checked") elem.checked = true + else elem.checked = false; + } + else { + if(!defVal) defVal = ""; + elem.value = defVal; + } + + var elShowDiff = utils.getParent(elem); + if(utils.hasClass(elShowDiff, "nondef")) { + utils.removeClass(elShowDiff, "nondef"); + } + //alert(elem.id + " " + $("NUM_DIFFS").value); +} + +function newResultsWinInit() { + jQuery("[class='newwin']").each(function(index) { + utils.addEvent(this, "click", setResultsTarget, false); + }); +} + +function resetOrganismSuggest(orgEntryElem) +{ + //suggestHint is in the hidden field used for SRA + var defaultMessage = ($("suggestHint")) ? $("suggestHint").value : "Enter organism name or id--completions will be suggested"; + var suggestHint = $("qorganism").getAttribute("suggestHint"); + if(suggestHint) defaultMessage = suggestHint; + if(orgEntryElem.value == "") { + orgEntryElem.value = defaultMessage; + } + if(orgEntryElem.value == defaultMessage) { + utils.addClass(orgEntryElem,"orgHint"); + } +} + +function setupOrganismSuggest(orgEntryElem) +{ + resetOrganismSuggest(orgEntryElem); + utils.addEvent(orgEntryElem, "focus", function() { + clearOrgSuggest(orgEntryElem); + }, false); +} + +function clearOrgSuggest(orgEntryElem) +{ + if(utils.hasClass(orgEntryElem,"orgHint")) { + orgEntryElem.value=""; + utils.removeClass(orgEntryElem,"orgHint"); + } +} + +function InitCustomButton(bn) +{ + utils.addEvent(bn, "mouseover", function() {this.src = this.getAttribute("mouseovImg");}, false); + utils.addEvent(bn, "mouseout", function() {this.src = this.getAttribute("mouseoutImg");}, false); + utils.addEvent(bn, "mousedown", function() {this.src = this.getAttribute("mousedownImg");}, false); + utils.addEvent(bn, "mouseup", function() {this.src = this.getAttribute("mouseupImg");}, false); +} + +function showHideElem(id,hide) +{ + if($(id)) { + if(hide) { + if(!utils.hasClass($(id),"hidden")) utils.addClass($(id), "hidden"); + } + else { + if(utils.hasClass($(id),"hidden")) utils.removeClass($(id), "hidden"); + } + } +} + +function resetOrganismControls(orgEntryElem) { + resetOrganismSuggest(orgEntryElem); + if ($("orgExcl")) $("orgExcl").checked = false; + utils.replaceInHtml("", $("orgs")); + if ($("frOrgs")) utils.replaceInHtml("", $("frOrgs")); + if ($("numOrg")) $("numOrg").value = 1; +} + +function AddOrgRow(e,orgName,exclName) { + e = e || window.event; + utils.preventDefault(e); + var checkedExclude = new Array(); + var orgDict = jQuery($($("qorganism"))).ncbiautocomplete("option","dictionary"); + orgDict = (!orgDict || orgDict == "") ? "taxids_sg" : orgDict; + var len = $("qorganism").getAttribute("size"); + + var newOrgFieldID = "qorganism" + $("numOrg").value; + var newOrgField = "
"; + if (exclName != "") { + newOrgField += "" + + "" + + ""; + } + newOrgField += "
"; + if (navigator.userAgent.match(/ie/i)) { + for (i = 1; i < $("numOrg").value; i++) { + if ($("orgExcl" + i)) checkedExclude[i] = $("orgExcl" + i).checked; + } + } + if (!navigator.userAgent.match(/firefox/i)) { + jQuery($($(orgs))).append(newOrgField,true); + } + else { + utils.insertInHtml(newOrgField, $("orgs")); + } + + if (navigator.userAgent.match(/ie/i)) { + for (i = 1; i < $("numOrg").value; i++) { + if ($("orgExcl" + i)) $("orgExcl" + i).checked = checkedExclude[i]; + } + } + setupOrganismSuggest($(newOrgFieldID)); + jQuery($($(newOrgFieldID))).ncbiautocomplete(); + $("numOrg").value++; +} + +function adjustOrgVal(orgEntryElem) +{ + //if (utils.hasClass($("searchForm").EQ_MENU, "orgHint")) $("searchForm").EQ_MENU.value = ""; + clearOrgSuggest(orgEntryElem); + if ($("numOrg")) { + for (i = 1; i < $("numOrg").value; i++) { + if ($("qorganism" + i)) { + clearOrgSuggest($("qorganism" + i)); + } + } + } +} + +function getUrlCompForEntryField(elem) { + var url = ""; + if (elem && elem.value != "") { + url = "&" + elem.name + "=" + escape(elem.value); + } + return url; +} + + +function getUrlCompForCheckedField(elem) { + var url = ""; + if (elem && elem.checked) { + url = "&" + elem.name + "=" + elem.value; + } + return url; + +} + +function getUrlCompForOptionsField(elem) { + var url = ""; + if (elem) { + url = "&" + elem.name + "=" + elem[elem.selectedIndex].value; + } + return url; +} + +function getUrlCompForMultiOptionsField(elem) { + var url = ""; + if (elem) { + for (i = 0; i < elem.options.length; i++) { + if (elem.options[i].selected) { + url += "&" + elem.name + "=" + elem.options[i].value; + } + } + } + return url; +} + + +utils.addEvent(window, 'load', newResultsWinInit, false); + diff -r 000000000000 -r a54279222d84 NCBI Blast reference example_files/blastReq.css --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NCBI Blast reference example_files/blastReq.css Mon May 19 09:43:54 2014 -0400 @@ -0,0 +1,332 @@ +#msgR .info { +background-color: #dfd; +padding: 4px; +border: solid 1px green; +color: green; +} + +dl.summary dt { +float: left; +width: 8em; +clear:left; +margin: 0; +text-align: right; +padding-right: 1em; +color: #666; +} + +dl.summary dd { +padding-left: 0.5em; +display: block; +margin-left: 7em !important; +margin: 0; +} +dl.summary dt, dl.summary dd { +margin-bottom: 0.5em; +} +a.help +{ +float:right; +font-size: 110%; +} + +dl.summary label { +display: inline; +} + +dl.summary tr th label { +padding: 0; +margin-right:0; +} +table.options { +border: solid 1px #ccc; +border-right: solid 1px #ccc; +} + +table.options td, +table.options td.frh { +font-size: 90%; +_font-size: 85%; +} + +table.options label.rb { +border-right: solid 1px #ccc; +margin-right: 0.5em; +padding-right: 2.0em; +} + +table.options tr td { +_font-size: 90%; +padding-left: 0.5em; +} + +table.options { +/*border-collapse: collapse;*/ +margin-left: 0; +padding-left: 0; +width: 62em; +} + +table.options td label { +font-size: 90%; +} + +table.options th label, +table.options td label { +margin-right: 0; +_position: relative; +_top: -0.1em; +} + +table.options tr.hdr td, +table.options tr.hdr th { +padding: 2px; +border: solid 1px #ccc; +background-color: #ddd; +} + +table.options td, table.options td.frh { +padding: 0.25em 0; +vertical-align: center; +} + +table.options th { +padding-right: 1em; +text-align: right; +padding-left: 1em; +} + +/* +*:focus{ +background-color: white !important; +} +*/ + +table.options select,table.options input, #graphic input{ +border: solid 1px #888; +padding: 1px; +} + +select { +font-size: 90%; +} + +select option { +padding-right: 0.5em; +} + +input.cb, table.options input.cb { +border: none; +} + +select { +margin-right:1em; +} + +table.options tr { +background-color: #eee; +} + +table.options tr.odd { +background-color: #e0e0e0; +} + +table.options th { + +background-color: white; +} + +table.options tr.paramSet td +{ + border-top: solid 2px white; +} + + + + +.resetAll +{ +font-weight: normal; +padding: 0.5em; +font-size: 90%; +margin-left:5em; +} + +.button { +background-color: #ccc; +padding: 0.25em 0.25em; +color: black; +border: outset 3px #eee; +_border: outset 3px #eee; +font-size: 90%; +_padding:0; +font-weight: bold; +height:25px; +_height:22px; +} + +.fbtn { +margin-bottom: 0.5em; +} + +.note { +font-size: 80%; +color: green; +background-color: #ffc; +margin-left: 2em; +padding: 3px; +} +.instr { + margin-left: 1em; + color: #666; +font-size: 90%; +} +.smaller { +font-size: 90%; +font-weight: normal; +} + +/* Results Page styles */ + +#ridRes +{ + background-color: #FC9; + padding:5px 5px; +} + + +span dd.hidden,dt.hidden,dd.hidden span +{ + display:none; +} + +dl.query .query, +dl.title .title, +dl.entrez .entrez, +dl.db .db +{ + display:block; +} + + +dl.entrez span.entrez +{ + display:inline; +} + +.hidden { +display: none; +} +.hide { +display: none; +} +.shown { +display: block; +} + + + +table.megaBlast tr.psiBlast, +table.blastn tr.psiBlast, +table.blastx tr.psiBlast, +table.tblastn tr.psiBlast, +table.tblastx tr.psiBlast, +table.discoMegablast tr.psiBlast +{ +display: none; +} + + +table.GlobalAln .xgl, +body.GlobalAln div.xgl, +body.GlobalAln dt.xgl, +body.GlobalAln dd.xgl, +body.GlobalAln span.xgl, +body.GlobalAln table.xgl +{ +display: none; +} + +.dispType +{ + /*background-color:White; + border:solid 1px black;*/ + border-top:solid 2px gray; + border-left:solid 2px gray; + font-size:90%; + padding-left:2px; + +} + +.newwin { +border: none; +} + +table.options .helplink +{ + font-weight:bold; + position:absolute; + right:0; +} + +div#query label +{ + display: inline; + font-weight:bold; + padding-right:1em; +} +#NEW_VIEW +{ + _margin-left:-2px; +} + + +table.blastp *.blastn, +table.psiBlast *.blastn, +table.phiBlast *.blastn, +table.blastx *.blastn, +table.tblastn *.blastn, +table.tblastx *.blastn +{ +display: none; +} + +#formatTable th.col1 { +width: 8em; +vertical-align: top; +} +/* +#formatTable .helplink span { +position: relative; +} +*/ +#org +{ + margin-top:2em; +} +#qorganism +{ + /*display:block;*/ +} +.fi +{ + position:relative; +} + +a#organismHelp +{ + margin-top:-1.5em; +} + +table.options tr.paramSet td.hd { +padding-right: 1em; +text-align: right; +padding-left: 1em; +background-color:White; +font-weight:bold; +border-top:none; +} +.oExcl +{ + margin-left:2px; +} diff -r 000000000000 -r a54279222d84 NCBI Blast reference example_files/blastRes.css --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NCBI Blast reference example_files/blastRes.css Mon May 19 09:43:54 2014 -0400 @@ -0,0 +1,262 @@ +a#refPage +{ + margin-left:3em; +} + +a.resLink +{ + margin-left:1em; + display:none; +} + +a.resLinkhidden +{ + display:none; +} + + +#cddResults +{ + float:right; + margin-top:-2em; + margin-right:1em; + color:#336699; + font-size:100%; +} + +#cddResults.showing { + background-image: url(images/down.gif); +} + + + +div.inlineDiv +{ + display:inline; +} + +span.reslink +{ + display:none; +} + +div.statPage *.statPage, +div.resPage *.resPage +{ + display:inline; +} + +div.resHeader *.hidden +{ + display:none; +} + +#cddInfo +{ + text-align:center; +} +#cddDesc +{ + font-weight:bold; +} +div#desctbl +{ +border: solid 1px #018aac; +/*min-width: 1000px;*/ +margin: none; +width: 100%; +background-color:White; +/*line-height:0; +_line-height:0;*/ +} + +table#descs +{ +font-family: Verdana, Sans-Serif; +font-size: 90%; +_font-size: 86%; +border-collapse: collapse; +/*min-width: 600px;*/ +width: 100%; +} + +table#descs th a { +text-decoration: none; +color: #00c; +} + +table#descs th a:visited { +color: #00c; +} + +table#descs th a:hover {position: relative; +text-decoration: underline; +} + +table#descs tr th.l, +table#descs tr td.l { +text-align: left; +} + +table#descs tr th.sp { +background-color: #def; +} + +table#descs tr th, +table#descs tr td { +text-align: center; +padding: 1px 4px; +} + +table#descs tr.first th { +padding-left:18px; +border-left: solid 1px #A0ceff; +border-top: solid 1px #A0ceff; +border-bottom: solid 1px #018aac; +border-right: solid 1px #018aac; +padding-right: 8px; +/*background-color: #01d5ff;*/ +background-color: #9cf; +/*font-size: 92%;*/ +white-space:normal; +line-height: 1.2em +} + + +table#descs td { +border: solid 1px #ccc; +border-width: 0px 1px; +white-space:nowrap; +overflow: hidden; +} + +.slink { +font-size: 90%; +font-weight: normal; +} + +table#descs tr.first th.sel { +background: #9cf url(images/up.gif) no-repeat center left; +padding-left: 18px; +padding-right: 18px; +} + +div.lim +{ +/*overflow: hidden;-this used to work in Firefox 2- comment for now and set the width */ +width: 35em; +display: inline-block; +height: 1.3em; +} + +table#descs tr:hover { +background-color: #def; +} + +pre +{ + font-size:110%; + _font-size:100%; + line-height:1; +} + +#msg +{ + white-space:normal; + border-color:#cccccc; + padding:0; + margin: 0; + margin-top:2px; +} +#msg li +{ + display:none; + padding:0; + margin: 0; + text-indent: 0; +} +#msg li.warning, #msg li.error ,#msg li.info +{ + display:block; +} + +#msg ul +{ + margin:0; + padding:0; +} + +table#statInfo +{ + border: solid 1px #ccc; + background-color: #eee; + width: 100%; +} + +table#statInfo tr.odd { +background-color: #e0e0e0; +} + +.READY, .UNKNOWN +{ + display:none; +} + +p.WAITING +{ + margin-top:1em; +} + +#frmPage +{ + margin-left:1em; +} + +span.Gene_PubMedLinks +{ + color: Green; font-weight: bold; +} + +ul.msg li p +{ + display:none; +} + +.msg li p.warning, .msg li p.error, .msg li p.success,.msg li p.info +{ + display:block; +} + +.mdlbox +{ + white-space:pre; + background-color:Transparent; + border:none; +} + +#blastErr +{ + white-space:normal; +} + + + +#RSIFrameNoRes,#RSIFrameDesc,#RSIFrameAln +{ + border:none; + width:519px; + height:35px; + margin:0px auto; +} + + +a.ui-ncbitoggler.hidden, a.ui-ncbitoggler-open.hidden +{ + display:none; +} + +.smn { + display: inline-block; + height: 16px; + width: 16px; +} diff -r 000000000000 -r a54279222d84 NCBI Blast reference example_files/dynFormatRes.css --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NCBI Blast reference example_files/dynFormatRes.css Mon May 19 09:43:54 2014 -0400 @@ -0,0 +1,623 @@ +/* style changes for redesign begin*/ +a.gbd +{ + text-decoration:none; +} + +tr.dflLnk td span +{ + font-size:78%; + display:none; + text-align:center; +} +a.dflSeq +{ + color:#369; + text-decoration:underline; + width:auto; +} +table.defln tr.dflLnk a +{ + margin-right:auto; + padding-left:0; +} + +.alnParLinks +{ + float:right; +} + +.alnSeqLinks +{ + float:right; + margin-right:1em; +} + + +.seqlinks select +{ + padding:0; +} + +.dlfRow div +{ + font-size:90%; +} + +.dlfRow +{ + display:inline; + font-size:110%; +} + +.dlfRow.hidden +{ + display:none; +} +.dlfRow label +{ + font-size:87%; + display:inline; + color:#606060; + font-weight:bold; +} + +.dlfRow span.r label +{ + padding-left:0.8em; +} + + +div.relInf +{ + font-family: Verdana, Sans-Serif; + font-size: 80%; + float:right; + width:21%; + border-top:solid 2px gray; + margin-top:-1em; + margin-right:3.5em; + left:3em; + max-width:25em; + padding-left:1em; + position:relative; + white-space:normal; +} + +div.relInf a +{ + padding-right:0.2em; +} + +.rlLink +{ + padding-left:0.2em; +} +.relInf label +{ + font-size:110%; + color:brown; + font-weight:bold; +} +div#content +{ + min-width:70em; +} + +.dflLnk a +{ + font-size:90%; +} +a.dflSeq +{ + width:auto; + font-weight:normal; +} + + +#cntDesc,#cntDesc_psiw +{ + margin-bottom:0.2em; + display:inline-block; + width:20em; +} +#cntDesc span,#cntDesc_psiw span +{ + margin-right:0.5em; +} + +#cntDesc a,#cntDesc input,#cntDesc_psiw a,#cntDesc_psiw input +{ + margin-left:0.5em; +} + +#cntSelNone,#cntShAll +{ + margin-left:0.2em; +} + +.toolsCtr +{ + color:Blue; +} + +table.ui-ncbigrid th span.slink a +{ + display:inline; + padding-right: 0; +} +table.ui-ncbigrid th.sp +{ + font-weight:bold; +} + +table.ui-ncbigrid th span.slink +{ + margin-left:0.2em; +} + +table.ui-ncbigrid td { + white-space:nowrap; +} +table.ui-ncbigrid td.c3 +{ + /*padding-left:0.8em;*/ +} +table.ui-ncbigrid caption +{ + font-size:0; + line-height:0; +} +#content h3.cap,#content h3.cap a.ui-ncbitoggler.ui-widget, #content h3.cap a.ui-ncbitoggler-open +{ + color:#4d4d4d; + text-align:left; + margin:0 0 0.5em 0; +} + +#content div.cap,#content div.cap a.ui-ncbitoggler.ui-widget, #content div.cap a.ui-ncbitoggler-open +{ + color:#4d4d4d; + text-align:left; + margin:0 0 0.5em 0; + letter-spacing:-1px; + font-size:110%; + font-weight:bold; +} + +#descriptions div.caption-exists { + margin: 0; +} + +/**********decrition toolbar styles *********/ + +div.cnf { + -moz-border-bottom-colors: none; + -moz-border-image: none; + -moz-border-left-colors: none; + -moz-border-right-colors: none; + -moz-border-top-colors: none; + background: url("images/cnf.png") repeat scroll 0 0 transparent; + border-style: solid none none; + border-width: 1px medium medium; + /*clear: left;*/ + height: 22px; + /*overflow: auto;*/ + width: 100%; +} + +ul.ui-ncbilocalnav li.has-child a.button_config { + background: url("/portal/portal3rc.fcgi/3493904/img/81796") no-repeat scroll right center transparent !important; + width: 22px; + height:22px; + margin-left:12em; +} + +#li-config +{ + float:right; + width:17em; +} +div#descTblCtrl ul.ui-ncbilocalnav li +{ + border-right:none; +} + + +.cfg +{ + font-size:90%; +} + + +.oneSeqAln .hsp label +{ + color:#606060; + font-size:95%; + padding-right:0.5em; +} + +.oneSeqAln pre +{ + margin-top:0.5em; +} + +.aln_feat label +{ + color: #606060; + font-size: 95%; + padding-right: 0.5em; +} +.oneSeqAln .dflLnk.aln_feat +{ + padding-bottom:1em; +} +div.oneSeqAln h4 +{ + border:none; + font-size:100%; + font-weight:normal; + letter-spacing:normal; + margin:0; +} + +.oneSeqAln .dflLnk +{ + width:56em; +} +.aln_feat a +{ + margin-left:1em; + display:block; +} +.dflLnk.aln_feat div +{ + /*display:inline-block; */ + margin-left:5em; + margin-top:-1em; +} +.aln_frame.shown +{ + display:block; +} +/*align params styles change */ + +table.alnParams +{ + border-left:none; + border-right:none; + margin-top:0.5em; + width:49em; +} + +table.alnParams th +{ + background-color:Transparent; + border:none; + text-align:left; +} + +table.alnParams td +{ + border:none; +} + + +.alnAll +{ + line-height:normal; + margin-top:1em; +} + +.alnAll div +{ + width:70%; +} + +/**new config staff begin**/ +.popDl +{ + display:none; +} +.popDl div +{ + margin-top:0.5em; +} +.popDl div.tl +{ + margin-top:0; + font-weight:bold; +} +a.button_config { + background: url("images/cnfButn.png") no-repeat scroll right center transparent !important; + width: 22px; + height:22px; + margin-left:12em; + float:right; +} + +a.toolsCtr,span.csLinks a +{ + margin-left:8px; + float:left; + cursor:pointer; +} + +a.toolsCtr[disabled] { + cursor: default; +} + + +a.toolsCtr SPAN +{ + color: #14376c; + /*line-height: 22px;*/ + padding-left: 15px; + background-repeat: no-repeat; + background-position:left center; +} + +a.toolsCtr[disabled] SPAN,a.toolsCtr[disabled] +{ + color:#C2C2C2; +} + +a.dnld span +{ + background-image: url("images/dndl.png"); +} + +a.dnld[disabled] span +{ + background-image: url("images/dndl_dsb.png"); +} + +a.dialog +{ + padding-right: 18px; + background:transparent url(images/dialog.png) no-repeat scroll right center; + text-decoration:none; +} + +a.dialog[disabled] { + background-image: url("images/dialog_dsb.png"); +} + + +a.alnNav span +{ + background-image: url("images/align_Normal.png"); +} + +a.alnNav +{ + text-decoration:none; +} + + +a.navNext span +{ + background-image: url("images/next_Normal.png"); +} + + +a.navNext[disabled] span +{ + background-image: url("images/next_Inactive.png"); +} + + +a.navPrev span +{ + background-image: url("images/prev_Normal.png"); +} + + +a.navPrev[disabled] span +{ + background-image: url("images/prev_Inactive.png"); +} + + +a.navBack span +{ + background-image: url("images/table_Normal.png"); +} + +.alnRn +{ + float:left; +} + + +/* styles to change per discusssion with Mark begin*/ +.dflLnk a +{ + padding-left:0; +} + + +table.ui-ncbigrid th { + padding-left:0.3em; + padding-right:0; + text-align:center; +} + +table.ui-ncbigrid td { + padding-left:0.4em; + padding-right:0.4em; + text-align:center; +} + +table.ui-ncbigrid td.c2,table.ui-ncbigrid td.c1 { + text-align:left; +} + +table.ui-ncbigrid td.c3{ + padding:0.363em 0.25em; +} + + +table.ui-ncbigrid th a { + padding-right: 5px; +} +table.ui-ncbigrid th.c0 +{ + width:25px; + padding:0; +} + +.dflnDth +{ + width:100%; +} +div.lim { + width: 14em; +} + +table.ui-ncbigrid th.c8,table.ui-ncbigrid th.c9 { + padding-right: 0.3em; +} +.c8,.c9 +{ + font-size:80%; +} + + +td.lim.l.c2,td.lim.l.c1 +{ + overflow:hidden; +} +a.spr +{ + border-right:none; +} + + +.psiInp +{ + margin-left:1em; + margin-top:0.5em; +} + + +.c8 input +{ + border:none; +} +table.ui-ncbigrid td.c8 +{ + padding-left:1.5em; +} + +tr.psi_new td +{ + background-color:#FFFF99; + border-top:solid 4px white; + border-spacing:3px; + border-collapse:collapse; + line-height:normal; +} +/* accessibility setting */ +tr.dflLnk td span.psiNw,tr.first th span,a.button_config span, a span.accsb,.dflLnk label.accsb +{ + display:inline; + position:absolute; + left:-9999px; +} + +div.tgl +{ + margin-top:-1em; +} +.shcl +{ + float:right; +} + +/* styles to change per discusssion with Mark end*/ + +.alnRn a +{ + padding-right:1em; +} +.alnAll .moreHsps +{ + font-family: Verdana, Sans-Serif; + font-size: 75%; + margin-top:-2.5em; + width:58%; +} +.erm +{ + background-color:#FFFFCC; + padding:0.5em; +} + +#debug,.ind,.alnMsgS .db,.erm .db +{ + display:none; +} + +.tmsAln label +{ + font-size:93%; + display:inline; + color:#606060; + font-weight:bold; +} +.alnAll .tmsAln, .tmsAln div +{ + width:100%; + margin-bottom:-1em; +} +.tmsAlnPar +{ + margin-top:-1em; +} +/*debug info styles begin */ + + +/* use those styles only in debug version + +.alnMsg +{ + border:solid 1px black; +} + +.alnMsgS.hidden,.alnMsgS .db +{ + display:block; +} + +.oneSeqAln +{ + border:1px solid #C8C8C8; +} + +#debug,tr.dflLnk td span.ind +{ + display:inline; +} +.c0 +{ + width:30px; +} +/*debug info styles end */ + + + +/**new config staff end**/ +/* +ul.ui-ncbilocalnav li, ul.ui-ncbilocalnav { + background-color: #F4F4F4; + background-image: -moz-linear-gradient(center top , #FFFFFF, #F4F4F4); +} +ul.ui-ncbilocalnav li { + border-right: 1px solid #C4C4C4; +} +*/ +/**********decrition toolbar styles end*********/ + + +/* style chenges for redesign end*/ diff -r 000000000000 -r a54279222d84 NCBI Blast reference example_files/firefox-descriptions.css --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NCBI Blast reference example_files/firefox-descriptions.css Mon May 19 09:43:54 2014 -0400 @@ -0,0 +1,3 @@ +table.dbInfo caption { + +} \ No newline at end of file diff -r 000000000000 -r a54279222d84 NCBI Blast reference example_files/format.js --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NCBI Blast reference example_files/format.js Mon May 19 09:43:54 2014 -0400 @@ -0,0 +1,270 @@ + +function UpdateDisplayTypes(displayTypes) { + dispMenu = displayTypes.options; + for(i=0; i < dispMenu.length; i++) { + //if(!utils.hasClass(displayTypes,"psiBlast") && !utils.hasClass(displayTypes,"phiBlast") || + if($("stepNumber").value == "" || $("stepNumber").value < 2) { + if(dispMenu[i].value.indexOf("PSSM") != -1) { + dispMenu[i--] = null; + //break; + } + } + } +} + +function GetIndexByValue(selectElem,val) { + var idx = 0; + var opts = selectElem.options; + for(i=0; i < opts.length; i++) { + if(opts[i].value == val) { + idx = i; + break; + } + } + return idx; +} + +function resetAdvView(show) +{ + var advView = $("advView"); + if(show) { + if(utils.hasClass(advView, "hidden")) { + utils.removeClass(advView, "hidden"); + } + } + else { + utils.addClass(advView, "hidden"); + } +} + + +function ShowOrHide(hide,elem) +{ + if(hide) { + if(!utils.hasClass(elem, "hidden")) { + utils.addClass(elem, "hidden"); + } + } + else { + if(utils.hasClass(elem, "hidden")) { + utils.removeClass(elem, "hidden"); + } + } +} + +function UpdateFormatTypes(form) { + var selectedObjType = form.FORMAT_OBJECT[form.FORMAT_OBJECT.selectedIndex].value; + var hideAdvView = false; + bioseqFormatHide = true; + pssmFormatHide = true; + pssmScFormatHide = true; + formatTypeHide = true; + if (selectedObjType == "Alignment") { + formatObjectSelectedIndex = 0; //HTML + formatTypeHide = false; + hideAdvView = true; + } + if (selectedObjType == "PSSM") { + formatObjectSelectedIndex = GetIndexByValue(form.FORMAT_TYPE,"Text"); + pssmFormatHide = false; + } + if (selectedObjType == "PSSM_Scoremat") { + formatObjectSelectedIndex = GetIndexByValue(form.FORMAT_TYPE,"ASN.1"); + pssmScFormatHide = false; + } + else if (selectedObjType == "Bioseq") { + formatObjectSelectedIndex = GetIndexByValue(form.FORMAT_TYPE,"ASN.1"); + bioseqFormatHide = false; + } + form.FORMAT_TYPE.selectedIndex = formatObjectSelectedIndex; + ShowOrHide(formatTypeHide,form.FORMAT_TYPE); + if ($("bioseqFormat")) { + ShowOrHide(bioseqFormatHide,$("bioseqFormat")); + $("bioseqFormat").readOnly=true; + } + if ($("pssmFormat")) { + ShowOrHide(pssmFormatHide,$("pssmFormat")); + $("pssmFormat").readOnly=true; + } + if ($("pssmScFormat")) { + ShowOrHide(pssmScFormatHide,$("pssmScFormat")); + $("pssmScFormat").readOnly=true; + } + resetAdvView(hideAdvView); +} + +function ResetForm() +{ + //var defValNodes = cssQuery(".reset"); + defValNodes = $("FormatForm").elements; + for(i=0; i < defValNodes.length; i++) { + if(utils.hasClass(defValNodes[i],"reset")) + setDefalValue(defValNodes[i]); + } + if ($("FormatForm").FORMAT_OBJECT.type == "select-one") { + UpdateFormatTypes($("FormatForm")); + UpdateDisplayTypes($("FormatForm").FORMAT_OBJECT); + } + if($("FormatForm").RUN_PSIBLAST.checked) setDefalValue($("FormatForm").I_THRESH) + else $("FormatForm").I_THRESH.value=""; + //resetOrganismSuggest($("FormatForm").FORMAT_ORGANISM); + resetOrganismControls($("FormatForm").FORMAT_ORGANISM); + //TO DO: add threshold +} + +function LimitByHitlistSize(list) +{ + var listBreak = false; + var optSel = false; + for(i=0; i < list.options.length; i++) { + var optVal = parseInt(list.options[i].value ,10); + var hitListSize = parseInt($("maxNumSeq").value ,10); + if(list.options[i].selected) optSel = true; + if(optVal >= hitListSize) { + if(!optSel) {list.options[i].selected = true;} + list.options.length = i + 1; + break; + } + } +} + +function AddFormatOrgField(e) { + AddOrgRow(e, "FORMAT_ORGANISM", "FORMAT_ORG_EXCLUDE"); +} + +function initSubmit() { + + +} + +function adjustFormatOptions() +{ + var alignView = $("FormatForm").ALIGNMENT_VIEW; + var formatType = $("FormatForm").FORMAT_TYPE; + var queryAnch = formatType[formatType.selectedIndex].value == "HTML" && (alignView[alignView.selectedIndex].value != "Pairwise" && alignView[alignView.selectedIndex].value != "PairwiseWithIdentities"); + var dynFormatQA = !$("FormatForm").OLD_VIEW.checked && queryAnch; + dynFormatPW = !$("FormatForm").OLD_VIEW.checked && formatType[formatType.selectedIndex].value == "HTML" && (alignView[alignView.selectedIndex].value == "Pairwise" || alignView[alignView.selectedIndex].value == "PairwiseWithIdentities"); + + UpdateDescriptions(dynFormatPW); + if (dynFormatPW) { + jQuery("#frmAln").addClass("hidden"); + if (!utils.hasClass($("shl"), "hidden")) jQuery("#shl").addClass("hidden"); //hide SHOW_LINKOUT + jQuery("#gts").addClass("hidden"); //hide GET_SEQUENCE + jQuery("#scf").removeClass("hidden");//show CDS_FEAT + $("FormatForm").SHOW_LINKOUT.checked = true; + } + else { + if(dynFormatQA) $("FRM_ALIGNMENTS").selectedIndex = $("FRM_DESCRIPTIONS").selectedIndex; + + jQuery("#frmAln").removeClass("hidden"); + if (dynFormatQA) { + if (!utils.hasClass($("shl"), "hidden")) jQuery("#shl").addClass("hidden"); //hide SHOW_LINKOUT + } + else { + jQuery("#shl").removeClass("hidden"); + } + if (queryAnch) { + jQuery("#scf").addClass("hidden"); //hide CDS_FEAT + } + else {//pairwise old_view=false + jQuery("#scf").removeClass("hidden"); //hide CDS_FEAT + } + jQuery("#gts").removeClass("hidden"); //GET_SEQUENCE + } + if ($("blastSpec").value == "VecScreen") { + adjustVecscreen(dynFormatPW); + } +} + +function adjustVecscreen(dynFormatPW) +{ + var dfltDescrInd = 0; //0 + var dfltDynDescrInd = 5; //1000 + var dfltAlnInd = 6; //1000 + if (dynFormatPW) { + utils.addClass($("lr"), "hidden"); + $("FRM_DESCRIPTIONS").selectedIndex = dfltDynDescrInd; + } + else { + utils.removeClass($("lr"), "hidden"); + $("FRM_DESCRIPTIONS").selectedIndex = dfltDescrInd; + } + $("FRM_ALIGNMENTS").selectedIndex = dfltAlnInd; +} + + +function UpdateDescriptions(removeZero) +{ + if (removeZero) { + dispMenu = $("FormatForm").DESCRIPTIONS; + dispMenu.remove(0); + } + else { + dispMenu = $("FormatForm").DESCRIPTIONS; + if (dispMenu.options[0].value != "0") { + if (navigator.userAgent.match(/ie/i)) { + dispMenu.add(new Option("0", "0"), 0); + } + else { + dispMenu.add(new Option("0", "0"), dispMenu[0]); + } + } + } +} + +function InitDynFormatOptions() +{ + if ($("OLD_VIEW")) { + utils.addEvent($("FormatForm").OLD_VIEW, "click", adjustFormatOptions, false); + utils.addEvent($("FormatForm").ALIGNMENT_VIEW,"change", adjustFormatOptions, false); + utils.addEvent($("FormatForm").FORMAT_TYPE, "change", adjustFormatOptions, false); + adjustFormatOptions(); + } +} + +function InitFormatPage() +{ + if ($("FormatForm").FORMAT_OBJECT.type == "select-one") { + UpdateDisplayTypes($("FormatForm").FORMAT_OBJECT); + UpdateFormatTypes($("FormatForm")); + list = $("FormatForm").FORMAT_OBJECT; + utils.addEvent(list, "change", function() { + UpdateFormatTypes($("FormatForm")); + }, + false); + } + utils.addEvent($("resetAll"), "click", ResetForm, false); + if($("maxNumSeq") != null) { + if($("maxNumSeq").value != "") { + LimitByHitlistSize($("FormatForm").DESCRIPTIONS); + LimitByHitlistSize($("FormatForm").ALIGNMENTS); + LimitByHitlistSize($("FormatForm").NUM_OVERVIEW); + } + } + setupOrganismSuggest($("FormatForm").FORMAT_ORGANISM); + utils.addEvent($("FormatForm"), "submit", function() { + adjustOrgVal($("FormatForm").FORMAT_ORGANISM);}, + false); + + if ($("addOrg")) utils.addEvent($("addOrg"), "click", AddFormatOrgField, false); + InitDynFormatOptions(); + /* add this code if decide image for View Report + var imgButtons = jQuery("[class='viewReport']"); + for (var i = 0; i < imgButtons.length; i++) { + var l = imgButtons[i]; + utils.addEvent(l, "click", function() {$("FormatForm").submit();}, false); + utils.addEvent(l, "mouseover", function() {l.src = l.getAttribute("mouseovImg");}, false); + utils.addEvent(l, "mouseout", function() {l.src = l.getAttribute("mouseoutImg");}, false); + utils.addEvent(l, "mousedown", function() {l.src = l.getAttribute("mousedownImg");}, false); + utils.addEvent(l, "mouseup", function() {l.src = l.getAttribute("mouseupImg");}, false); + } + */ +} + +utils.addEvent(window, 'load', InitFormatPage, false); + + + + + + diff -r 000000000000 -r a54279222d84 NCBI Blast reference example_files/formatRes.js --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NCBI Blast reference example_files/formatRes.js Mon May 19 09:43:54 2014 -0400 @@ -0,0 +1,1542 @@ +// JScript source code +/*************************new code begin *******************************************************/ + +function getHiddenFieldVal(elemName) { + var val; + var elem = document.getElementsByName(elemName); + if (elem) { + val = (elem.length > 1) ? elem[0].value : elem.value; + } + return val; +} + +function getHiddenFieldParamString(elemName) { + var ret = ""; + var val = getHiddenFieldVal(elemName); + if (val) { + ret = "&" + elemName + "=" + val; + } + return ret; +} + +function elementInViewport(el) { + if (!el) return; + var rect = el.getBoundingClientRect(); + + var myWidth = 0, myHeight = 0; + if (typeof (window.innerWidth) == 'number') { + //Non-IE + myWidth = window.innerWidth; + myHeight = window.innerHeight; + } else if (document.documentElement && (document.documentElement.clientWidth || document.documentElement.clientHeight)) { + //IE 6+ in 'standards compliant mode' + myWidth = document.documentElement.clientWidth; + myHeight = document.documentElement.clientHeight; + } else if (document.body && (document.body.clientWidth || document.body.clientHeight)) { + //IE 4 compatible + myWidth = document.body.clientWidth; + myHeight = document.body.clientHeight; + } + //window.alert('Width = ' + myWidth); + //window.alert('Height = ' + myHeight); + + + //return (rect.top >= 0 && rect.left >= 0 && rect.bottom <= window.innerHeight && rect.right <= window.innerWidth) + //return (rect.top >= 0 && rect.left >= 0 && rect.bottom <= myHeight && rect.right <= myWidth) + return (rect.top >= 0 && rect.bottom <= myHeight); +} + +function DisplayAlignFromDescription(elem) { + var alignView = $("FormatForm").ALIGNMENT_VIEW; + if (alignView[alignView.selectedIndex].value == "Pairwise" || alignView[alignView.selectedIndex].value == "PairwiseWithIdentities") { + DisplayDynamicAlign(elem); + } + else { + location.href = "#" + elem.getAttribute("seqID"); + } +} + +// ind="" gi="" id="deflnDesc_gi" href="#AlnHdrgi">desc +//
+function DisplayDynamicAlign(elem) { + var currGi = elem.getAttribute("gi"); + var currInd = elem.getAttribute("ind"); + var stat = elem.getAttribute("stat"); + if (!currInd || !currGi) return; + + if (!stat || stat == "") { + //Get 4(5) aligns before currInd and 4(5) aligns after + ReadCurrentSeqAligns(currInd, 5); + } + else if (stat == "read") { + var indexes = getCurrIndexRange(currInd); + if (indexes) { + var msgID = "alnShow_" + indexes[0]; + location.href = "#" + msgID; + } + } + else { + //error status handling + } +} + + +function goToNextAlign(dtrID, next) { + var currInd = parseInt($(dtrID).getAttribute("ind")); + var rid = $("Rid").value; + nextInd = (next) ? currInd + 1 : currInd - 1; + + if ($("deflnDesc_" + nextInd)) { + currGi = $("deflnDesc_" + nextInd).getAttribute("seqID"); + scrollToGI = currGi; + if (!$("deflnDesc_" + nextInd).getAttribute("stat") || $("deflnDesc_" + nextInd).getAttribute("stat") == "") { + + if (!next) { + ReadPrevSeqAligns(currInd, 5, scrollToGI); + } + else { + //Use this indexes = wasAlignRead(nextInd); to determine insertAfterID in ReadNextAligns!!! + ReadNextSeqAligns(currInd, 5, scrollToGI); + } + + } + else { + location.href = "#" + scrollToGI; + } + } +} + +function goToDefLine(dtrID) { + if ($("psiInp")) { + var tbl = jQuery($(dtrID)).parents(".jig-ncbigrid"); //parent table + togglerID = PsiBelowThresh(tbl[0].id) ? "showDescB1" : "showDescG1"; + jQuery($(togglerID)).ncbitoggler("open"); + } +} + +/* +readAln.rid = rid; +readAln.startIndex = parseInt(currInd); +readAln.numSeq = parseInt(maxNumAligns); + +readAln.insertAfterID = insertAfterID; +readAln.seqList = giList; +readAln.scrollToSeqID = scrollToGI; +*/ +function ReadNextSeqAligns(currInd, maxNumAligns, scrollToGI) { + var lastDispIdx = 0; + var rid = $("Rid").value; + + var readAln = new Object(); + readAln.seqList = ""; //giList + readAln.rid = rid; + + currInd = parseInt(currInd); + + if (currInd != 0 && $("deflnDesc_" + currInd)) { + var par = utils.getParent($("aln_" + $("deflnDesc_" + currInd).getAttribute("seqID"))); //"alnShowReal_ + //alert(par.id); + if (par) par = utils.getParent(par); //"alnShow_ + //alert(par.id); + if (par) readAln.insertAfterID = par.id; + } + else { + readAln.insertAfterID = "alnStart"; + } + + + + readAln.startIndex = currInd + 1; + readAln.numSeq = maxNumAligns; + + checkIfAlnExceedsThreshold(readAln, currInd, maxNumAligns, "next"); + + readAln.scrollToSeqID = (scrollToGI && scrollToGI != "") ? scrollToGI : ""; + readAln.hspSort = 0; + ReadSeqAlignByIndex(readAln); +} + +function ReadPrevSeqAligns(currInd, maxNumAligns, scrollToGI) { + var lastDispIdx = 0; + var rid = $("Rid").value; + + var readAln = new Object(); + readAln.seqList = ""; //giList + readAln.rid = rid; + + currInd = parseInt(currInd); + + + //sets readAln.insertAfterID and returns lastDispIdx; + //Find the index of the previously displayed alignment + lastDispIdx = getPrevDisplyedAlignInfo(currInd, readAln); + + readAln.startIndex = (currInd - lastDispIdx > maxNumAligns) ? (currInd - maxNumAligns) : lastDispIdx + 1; + readAln.numSeq = currInd - readAln.startIndex; //stopIndex = currInd + + checkIfAlnExceedsThreshold(readAln, currInd, readAln.numSeq, "prev"); + + readAln.scrollToSeqID = (scrollToGI && scrollToGI != "") ? scrollToGI : $("deflnDesc_" + (currInd)).getAttribute("seqID"); + readAln.hspSort = 0; + ReadSeqAlignByIndex(readAln); +} + +//When descriptions is clicked - display maxNumAligns before currInd and maxNumAligns after currInd +function ReadCurrentSeqAligns(currInd, maxNumAligns) { + var rid = $("Rid").value; + var readAln = new Object(); + readAln.seqList = ""; //giList + readAln.rid = rid; + + currInd = parseInt(currInd); + + + //sets readAln.insertAfterID and returns lastDispIdx; + //Find the index of the previously displayed alignment + var lastDispIdx = getPrevDisplyedAlignInfo(currInd, readAln); + + //lastDispIdx = parseInt(lastDispIdx); + readAln.startIndex = (currInd - lastDispIdx > maxNumAligns) ? (currInd - maxNumAligns) : lastDispIdx + 1; + readAln.numSeq = parseInt(maxNumAligns * 2); + + checkIfAlnExceedsThreshold(readAln, currInd, maxNumAligns, "curr"); + + readAln.scrollToSeqID = $("deflnDesc_" + currInd).getAttribute("seqID"); + readAln.hspSort = 0; + ReadSeqAlignByIndex(readAln); + g_DisableAutoCheck = true; + location.href = "#alnShow_" + readAln.startIndex; +} + + + + +function setupDynHSPParams(readAln) +{ + var currSeqInd = readAln.startIndex; + hspNum = parseInt($("deflnDesc_" + currSeqInd).getAttribute("hsp")); + alnLen = parseInt($("deflnDesc_" + currSeqInd).getAttribute("len")); + var maxDispLen = parseInt($("maxDispAlnLen").value);//20000 + var minDispLen = parseInt($("minDispAlnLen").value);//2000 + if (alnLen > maxDispLen) { + var lenPerMatch = alnLen / hspNum; + readAln.AlignDbPageSize = (lenPerMatch > minDispLen) ? 1 : Math.floor(minDispLen / lenPerMatch); + readAln.AlignDbPageNum = 0; + $("deflnDesc_" + currSeqInd).setAttribute("dynHsps", readAln.AlignDbPageSize); + } +} + + + +function getCurrSeqsAlnLen(currSeqInd) +{ + var alnLen = 0; + if ($("deflnDesc_" + currSeqInd) && (!$("deflnDesc_" + currSeqInd).getAttribute("stat") || $("deflnDesc_" + currSeqInd).getAttribute("stat") == "")) { + alnLen = $("deflnDesc_" + currSeqInd).getAttribute("len"); + } + alnLen = (alnLen) ? parseInt(alnLen) : 0; + return alnLen; +} + +function checkTotalAlignLen(startIndex,stopIndex) +{ + var dispAlnLen = 0; + var maxDispLen = parseInt($("maxDispAlnLen").value); + for (var i = startIndex; i <= stopIndex; i++) { + alnLen = getCurrSeqsAlnLen(i); + if (alnLen == 0) break; + dispAlnLen += alnLen; + } + return dispAlnLen; +} +//Get total align length for seq currSeqInd and +//"curr" surrounding countSeqs seqs + current, "prev" - previous countSeqs seqs, "next" - next countSeqs seqs +function getTotalAlignLen(readAln, currSeqInd, countSeqs, dispType) +{ + var startIndex = readAln.startIndex; + var stopIndex = readAln.startIndex + readAln.numSeq - 1; + if (dispType == "curr") {//checks countSeqs before and countSeqs after current, including current + startIndex = Math.max(startIndex, currSeqInd - countSeqs); + stopIndex = Math.min(stopIndex, currSeqInd + countSeqs); + } + else if(dispType == "prev") { + startIndex = Math.max(startIndex, currSeqInd - 1 - countSeqs); + stopIndex = currSeqInd - 1; + } + else {//next + stopIndex = Math.min(stopIndex, currSeqInd + countSeqs + 1); + } + var totAlnLen = checkTotalAlignLen(startIndex,stopIndex); + return totAlnLen; +} + +function checkIfAlnExceedsThreshold(readAln,currSeqInd,maxNumAligns, dispType) +{ + var maxDispLen = parseInt($("maxDispAlnLen").value); + var totAlnLen = 0; + var exc = false; + for (var numSeq = 0; numSeq <= maxNumAligns; numSeq++) { + totAlnLen = getTotalAlignLen(readAln, currSeqInd, numSeq, dispType); + if(totAlnLen > maxDispLen) { + break; + } + } + if (totAlnLen > maxDispLen) { + if (numSeq != 0) numSeq--; + if (dispType == "curr") { + readAln.startIndex = Math.max(readAln.startIndex, currSeqInd - numSeq); + //prev + 1(curr) + next + readAln.numSeq = (currSeqInd - readAln.startIndex) + 1 + numSeq; + } + else if (dispType == "prev") { + readAln.startIndex = Math.max(readAln.startIndex, currSeqInd - 1 - numSeq); + readAln.numSeq = numSeq + 1; + } + else { //"next" - readAln.startIndex stays + readAln.numSeq = numSeq + 1; + } + + if (readAln.numSeq == 1 && $("useAlignDB") && $("useAlignDB").value == "true") { + setupDynHSPParams(readAln); + } + + exc = true; + } + return exc; +} + + +//readAln.startIndex, readAln.numSeq, readAln.scrollToSeqID,readAln.insertAfterID should be set +function ReadSeqAlignByIndex(readAln) { + var numAligns = 0; + for (var i = readAln.startIndex; i < readAln.startIndex + readAln.numSeq; i++) { + + if (!$("deflnDesc_" + i)) { + break; + } + if (!$("deflnDesc_" + i).getAttribute("stat") || $("deflnDesc_" + i).getAttribute("stat") == "") { + currGi = $("deflnDesc_" + i).getAttribute("seqFSTA"); + if (readAln.seqList != "") readAln.seqList += ","; + readAln.seqList += currGi; + numAligns++; + } + else { + break; + } + } + if (readAln.seqList != "") { + readAln.numSeq = parseInt(numAligns); + ReadSeqAlignForSeqList(readAln); + } +} + + +var g_DisplayeAlignsRanges = ""; //String in the format start1-stop1,start2-stop2... +//Find the range of indexes of displayed alignments for currAlnInd +//Returns array of 2 startIndex, stopIndex +function getCurrIndexRange(currAlinInd) { + var currRange; + var ranges = g_DisplayeAlignsRanges.split(","); + for (var i = 0; i < ranges.length; i++) { + var indexes = ranges[i].split("-"); + if (currAlinInd >= parseInt(indexes[0]) && currAlinInd <= parseInt(indexes[1])) { + currRange = indexes; + break; + } + } + return currRange; +} + + +//Find the index of the previous displayed alignment +function getPrevDisplyedAlignInfo(currInd, readAln) { + readAln.insertAfterID = "alnStart"; + lastDispIdx = 0; + for (var i = currInd - 1; i >= 1; i--) { + indexes = getCurrIndexRange(i); + if (indexes) { + lastDispIdx = indexes[1]; + readAln.insertAfterID = "alnShow_" + indexes[0]; + break; + } + } + return parseInt(lastDispIdx); +} + + +//setReadStatus +function setSeqAlnReadStatus(readAln, status) { + for (var i = readAln.startIndex; i < readAln.startIndex + readAln.numSeq; i++) { + if ($("deflnDesc_" + i)) { + jQuery($($("deflnDesc_" + i))).attr("stat", status); + if (status == "disp") { + g_MaxDisplayedIndex = (i > g_MaxDisplayedIndex) ? i : g_MaxDisplayedIndex; + } + } + } +} + +/* +readAln.rid = rid; +readAln.seqList = giList; +readAln.startIndex = parseInt(idx); +readAln.insertAfterID = insertAfterID; +readAln.numSeq = parseInt(numSeq); +readAln.scrollToSeqID = scrollToGI; +*/ +function SendReadSeqAlinRequest(readAln) { + blastUrl = "t2g.cgi"; + + var rp = new RemoteDataProvider(blastUrl); + + + rp.onSuccess = function(obj) { + if ($("alignView")) utils.removeClass($("alignView"), "hidden"); + + if ($("alnShow_" + readAln.startIndex)) { + var moreHspsLink = getNextHspsLink(readAln); + jQuery($($("alnShowReal_" + readAln.startIndex))).html(obj.responseText + moreHspsLink, { + 'widgets': ['ncbipopper', 'ncbitoggler'], + 'configs': { + 'ncbipopper': { hasArrow: true, arrowDirection: 'top' } + } + }); + setSeqAlnReadStatus(readAln, "disp"); + jQuery($("alnMsg_" + readAln.startIndex)).addClass("hidden"); + //Saves start and stop indexes of loaded alignments in global variables + saveIdxesForAutomaticLoad(readAln); + jQuery($($("alnShowReal_" + readAln.startIndex))).find(".alnHdr").each(function(index) { + var seqID = this.getAttribute("seqID"); + if(seqID) initAlignBatch(seqID); + }); + + } + + if (readAln.scrollToSeqID) { + location.href = "#" + readAln.scrollToSeqID; + } + + }; + rp.onError = function(obj) { + if ($("alignView")) utils.removeClass($("alignView"), "hidden"); + jQuery($("alnMsg_" + readAln.startIndex)).addClass("hidden"); + $("alnShowReal_" + readAln.startIndex).innerHTML = "
Error loading alignment ...requests:" + this.iActiveRequests + " status:" + obj.status + + "Try again<\a>
"; + } + var params = constructURLParams(readAln); + if (readAln.numSeq == 1) { + params += "&TOTAL_HSPS=" + $("deflnDesc_" + readAln.startIndex).getAttribute("hsp"); + } + params += "&SEQ_LIST_START=" + readAln.startIndex; + + var formatParams = constructFormatParams(); + params += formatParams; + + //alert(params); + rp.Request(params); +} + + +function constructURLParams(readAln) { + var params; + + if ($("useAlignDB") && $("useAlignDB").value == "true") { + + var alignDbParams = "&USE_ALIGNDB=true"; + var batchID = document.getElementsByName("ALIGNDB_BATCH_ID"); + if (batchID) { + alignDbParams += getHiddenFieldParamString("ALIGNDB_BATCH_ID"); + alignDbParams += getHiddenFieldParamString("ALIGNDB_MASTER_ALIAS"); + alignDbParams += getHiddenFieldParamString("ALIGNDB_CGI_HOST"); + alignDbParams += getHiddenFieldParamString("ALIGNDB_CGI_PATH"); + } + alignDbParams += "&ALIGN_SEQ_LIST=" + readAln.seqList; + alignDbParams += "&HSP_SORT=" + readAln.hspSort; + + if (readAln.hasOwnProperty("AlignDbPageNum")) { + alignDbParams += "&ALIGNDB_PAGE_NUM=" + readAln.AlignDbPageNum; + alignDbParams += "&ALIGNDB_PAGE_SIZE=" + readAln.AlignDbPageSize; + alignDbParams += "&HSP_START=" + readAln.AlignDbPageSize * readAln.AlignDbPageNum; + } + + params = "CMD=Get&RID=" + readAln.rid + "&OLD_BLAST=false&DESCRIPTIONS=0&NUM_OVERVIEW=0&DYNAMIC_FORMAT=on" + alignDbParams; + } + else { + params = "CMD=Get&RID=" + readAln.rid + "&OLD_BLAST=false&DESCRIPTIONS=0&NUM_OVERVIEW=0&GET_SEQUENCE=on&DYNAMIC_FORMAT=on&ALIGN_SEQ_LIST=" + readAln.seqList + "&HSP_SORT=" + readAln.hspSort; + } + if ($("phiPtInd")) { + params += "&PHI_PTTRN_INDEX=" + $("phiPtInd")[$("phiPtInd").selectedIndex].value; + } + return params; +} + +/* +readAln.rid = rid; +readAln.seqList = giList; +readAln.startIndex = parseInt(idx); +readAln.insertAfterID = insertAfterID; +readAln.numSeq = parseInt(numSeq); +readAln.scrollToSeqID = scrollToGI; +*/ +/*1. Draw div with id="alnShow_index" class ="alnMsg" with the message listing gis nad indexes +2. Insert another div with id="alnShowReal_index and class="alnMsgR" +3. For "alnShow_index" set atrr indexes="startInd-stopInd" +4. Set global g_MaxReadMessageIndex - max index of displayed seqalign ??? - check this +5. Add string "startInd-stopInd" to g_DisplayeAlignsRanges - comma separated indexes +6. Send read request +*/ + +function ReadSeqAlignForSeqList(readAln) { + var text = "
Loading alignment... for sequences " + readAln.seqList; + var stopIndex = readAln.startIndex + readAln.numSeq - 1; + var useAlignDB = ($("useAlignDB") && $("useAlignDB").value == "true") ? "AlignDB=on " : ""; + text += " " + useAlignDB + "Reading indexes " + readAln.startIndex + "-" + stopIndex + "
"; + text += "
"; + var debugControl = "
"; + if (!$("debug")) { + jQuery($($("descriptions"))).before(debugControl); + } + if (!$("alnShow_" + readAln.startIndex)) { + jQuery($($(readAln.insertAfterID))).after(text); + jQuery($($("alnShow_" + readAln.startIndex))).attr("indexes", readAln.startIndex + "-" + stopIndex); + jQuery($($("alnShow_" + readAln.startIndex))).attr("seqlist", readAln.seqList); + g_MaxReadMessageIndex = (readAln.startIndex > g_MaxReadMessageIndex) ? readAln.startIndex : g_MaxReadMessageIndex; + setSeqAlnReadStatus(readAln, "read"); + $("debug").innerHTML += ", " + useAlignDB + "Reading indexes " + readAln.startIndex + "-" + stopIndex; + + if (g_DisplayeAlignsRanges != "") g_DisplayeAlignsRanges += ","; + g_DisplayeAlignsRanges += readAln.startIndex + "-" + stopIndex; + + SendReadSeqAlinRequest(readAln); + } + else if ($("alnShowReal_" + readAln.startIndex).innerHTML.indexOf("Error") != -1) { + jQuery($("alnMsg_" + readAln.startIndex)).removeClass("hidden"); + jQuery($("erm_" + readAln.startIndex)).remove(); + SendReadSeqAlinRequest(readAln); + } +} + + +function ReSubmitReadSeqAligns(e,currInd) { + var rid = $("Rid").value; + if ($("alnShow_" + currInd)) { + var indexRange = jQuery($("alnShow_" + currInd)).attr("indexes"); + var range = indexRange.split("-"); + + + var readAln = new Object(); + readAln.seqList = ""; //giList + readAln.rid = rid; + readAln.seqList = jQuery($("alnShow_" + currInd)).attr("seqlist"); + readAln.startIndex = parseInt(range[0]); + readAln.numSeq = parseInt(range[1]) - parseInt(range[0]) + 1; + readAln.hspSort = 0; + ReadSeqAlignForSeqList(readAln); + utils.preventDefault(e); + } +} + + +var g_MaxReadMessageIndex = 0; //alnShow_idx with the message, deflnDesc_idx with stat="read" +var g_MaxDisplayedIndex = 0; //deflnDesc_idx with stat="disp" - last one in the set of N +var g_DisableAutoCheck = false; + +var g_autoStartIdx = new Array(); +var g_autoStopIdx = new Array(); + +function saveIdxesForAutomaticLoad(readAln) { + var stopIndex = readAln.startIndex + readAln.numSeq - 1; + g_autoStartIdx.push(readAln.startIndex); //1,20,25 + g_autoStopIdx.push(stopIndex); //4,24,29 + $("debug").innerHTML += ", displaying indexes " + readAln.startIndex + "-" + stopIndex; +} + +function getNextHspsLink(readAln) +{ + var moreHspsLink = "" + if (readAln.hasOwnProperty("AlignDbPageNum")) { + var nextPageNum = readAln.AlignDbPageNum + 1; + var currHspInd = readAln.AlignDbPageSize * nextPageNum; + var argstring = readAln.startIndex + "," + currHspInd; + var currGi = $("deflnDesc_" + readAln.startIndex).getAttribute("seqId"); + var accs = $("deflnDesc_" + readAln.startIndex).getAttribute("accs"); + var totalHsps = $("deflnDesc_" + readAln.startIndex).getAttribute("hsp"); + var prevHspInd = readAln.AlignDbPageSize * nextPageNum; + var segs = (prevHspInd + 1) + "-" + (prevHspInd + readAln.AlignDbPageSize); + var moreHspsID = "nxHsp" + currGi + "_" + (prevHspInd + 1); + + moreHspsLink = $("dynHspTmpl").innerHTML.replace("@moreHspsID@", moreHspsID); + moreHspsLink = moreHspsLink.replace(/@accs@/g, accs); + moreHspsLink = moreHspsLink.replace("@argstring@", argstring); + moreHspsLink = moreHspsLink.replace(/@segs@/g, segs); + moreHspsLink = moreHspsLink.replace("@totalHSP@", totalHsps); + moreHspsLink = moreHspsLink.replace(/@alignDbPageSize@/g, readAln.AlignDbPageSize); + moreHspsLink = moreHspsLink.replace("@aln_prev_num@", prevHspInd); + moreHspsLink = moreHspsLink.replace("@alnSeqGi@", currGi); + } + return moreHspsLink; +} + + +function ReadNextHSPSet(currSeqInd, currHSPNum) { + var readAln = new Object(); + + readAln.rid = $("Rid").value; + readAln.seqList = $("deflnDesc_" + currSeqInd).getAttribute("seqFSTA"); + readAln.gi = $("deflnDesc_" + currSeqInd).getAttribute("seqId"); + dynHsps = $("deflnDesc_" + currSeqInd).getAttribute("dynHsps"); + readAln.startIndex = currSeqInd; + readAln.numSeq = 1; + if (dynHsps) { + readAln.AlignDbPageNum = parseInt(currHSPNum) / parseInt(dynHsps); + readAln.AlignDbPageSize = parseInt(dynHsps); //number of HSps to retrieve + } + if (currHSPNum != 0) { + readAln.scrollToSeqID = "hsp" + +readAln.gi + "_" + (parseInt(currHSPNum) + 1); + readAln.insertAfterID = "ar_" + readAln.gi + "_" + currHSPNum; + } + var sortLink = $("sa_" + readAln.gi); + readAln.hspSort = (sortLink) ? parseInt(sortLink[sortLink.selectedIndex].value) : 0; + SendReadSeqAlinSortHSPRequest(readAln); +} + +function ReadNextHSPSetEvt(e, currSeqInd, currHSPNum) { + ReadNextHSPSet(currSeqInd, currHSPNum); + utils.preventDefault(e); +} + + + +function checkAutoAlignArray() { + var stop = false; + var start = false; + var currAlignViewPos = $("alignView").getBoundingClientRect().top; + if (currAlignViewPos < g_alignViewPos) {//scrolling down + g_alignViewPos = currAlignViewPos; + if (g_DisableAutoCheck) { + g_DisableAutoCheck = false; + return; + } + for (i = 0; i < g_autoStopIdx.length; i++) { + if (elementInViewport($("alnHdr_" + $("deflnDesc_" + g_autoStopIdx[i]).getAttribute("seqID")))) { + //alert("Reading more aligns scrolling down!"); + var nextInd = parseInt(g_autoStopIdx[i] + 1); + var currInd = g_autoStopIdx[i]; + if ($("deflnDesc_" + nextInd) && (!$("deflnDesc_" + nextInd).getAttribute("stat") || $("deflnDesc_" + nextInd).getAttribute("stat") == "")) { + ReadNextSeqAligns(currInd, 5); + stop = true; + break; + } + } + } + if (stop) g_autoStopIdx.splice(i, 1); //delete index from the array + } + else if (currAlignViewPos > g_alignViewPos) {//scrolling up + g_alignViewPos = currAlignViewPos; + //here maybe return if autoStop found!!! + /* commenting automic read when scroll up */ + for (i = 0; i < g_autoStartIdx.length; i++) { + if (elementInViewport($("alnHdr_" + $("deflnDesc_" + g_autoStartIdx[i]).getAttribute("seqID")))) { + //alert("Reading more aligns scrolling up!"); + var currInd = g_autoStartIdx[i]; + //Check for condition here if go there at all!!! Check if do the same thing as for ReadNext!!!! + if (currInd > 1) { + ReadPrevSeqAligns(currInd, 5); + start = true; + break; + } + } + } + if (start) g_autoStartIdx.splice(i, 1); + } + /*end of comment*/ +} + +var g_alignViewPos = 0; + +function checkAutoAlignLoad() { + + + checkAutoAlignArray(); + + if (jQuery($($(window))).scrollTop() + jQuery($($(window))).height() >= jQuery($($(document))).height() - 100) { + //alert("bottom!"); + + if ($("alnShowReal_" + g_MaxReadMessageIndex) && $("alnShowReal_" + g_MaxReadMessageIndex).innerHTML != "") { + //if(!$("alnShow_" + maxReadMessageIndex)) {//g_MaxReadMessageIndex + ReadNextSeqAligns(g_MaxDisplayedIndex, 5); + } + } +} + + +function GetPatternLocResults() +{ + form = $("results"); + if (!form.PHI_PTTRN_INDEX) { + var el = document.createElement("input"); + el.name = "PHI_PTTRN_INDEX"; + el.value = $("phiPtInd")[$("phiPtInd").selectedIndex].value; + form.appendChild(el); + } + else { + form.PHI_PTTRN_INDEX.value = $("phiPtInd")[$("phiPtInd").selectedIndex].value; + } + form.submit(); +} + +function goToNextHSP(elem, next) { + var par = jQuery(elem).parent(); //parent span with class="alnParLinks" + var parts = par[0].id.split("_"); //"hsp_hspnum "hsp207524544_2" + if (parts[0].indexOf("nxHsp") != -1) { + parts[0] = parts[0].replace("nxHsp", "hsp"); + } + nextID = (next) ? parts[0] + "_" + (parseInt(parts[1]) + 1) : parts[0] + "_" + (parseInt(parts[1]) - 1) + + gotoElem = jQuery($(nextID)); + if (gotoElem[0]) { + a = jQuery(gotoElem).offset(); + window.scroll(0, a.top); + } + + else { + retrieveNextHSP(parts[0],parts[1]); + } + +} + + +//parts[0]//hsp, parts[1] hspnum +function retrieveNextHSP(currLinkID, currHSPNum) +{ + var desLineID = currLinkID.replace("hsp", "dtr_"); //tr id + var currSeqInd, totalHsps; + jQuery($($(desLineID))).find(".deflnDesc").each(function(index) { + currSeqInd = parseInt(this.getAttribute("ind")); + totalHsps = parseInt(this.getAttribute("hsp")); + dynHsps = this.getAttribute("dynHsps"); + }); + currHSPNum = parseInt(currHSPNum); + if (currHSPNum < totalHsps && dynHsps) { + ReadNextHSPSet(currSeqInd, currHSPNum); + } +} +/********Adding those functions back to formatRes.js to identify Uncaught ReferenceError: getUrlCompForCheckedField is not defined error********************************/ +function getUrlCompForEntryField(elem) { + var url = ""; + if (elem && elem.value != "") { + url = "&" + elem.name + "=" + escape(elem.value); + } + return url; +} + + +function getUrlCompForCheckedField(elem) { + var url = ""; + if (elem && elem.checked) { + url = "&" + elem.name + "=" + elem.value; + } + return url; + +} + +function getUrlCompForOptionsField(elem) { + var url = ""; + if (elem) { + url = "&" + elem.name + "=" + elem[elem.selectedIndex].value; + } + return url; +} +/****************************************/ + +function constructFormatParams() { + var formatParams = ""; + + if ($("queryList")) { + formatParams += "&QUERY_INDEX=" + $("queryList")[$("queryList").selectedIndex].value; + } + + + formatParams += getUrlCompForCheckedField($("FormatForm").SHOW_LINKOUT); + formatParams += getUrlCompForCheckedField($("FormatForm").SHOW_CDS_FEATURE); + formatParams += getUrlCompForCheckedField($("FormatForm").NCBI_GI); + formatParams += getUrlCompForOptionsField($("FormatForm").ALIGNMENT_VIEW); + formatParams += getUrlCompForOptionsField($("FormatForm").MASK_CHAR); + formatParams += getUrlCompForOptionsField($("FormatForm").MASK_COLOR); + formatParams += getUrlCompForEntryField($("FormatForm").EXPECT_LOW); + formatParams += getUrlCompForEntryField($("FormatForm").EXPECT_HIGH); + formatParams += getUrlCompForEntryField($("FormatForm").PERC_IDENT_LOW); + formatParams += getUrlCompForEntryField($("FormatForm").PERC_IDENT_HIGH); + formatParams += getUrlCompForEntryField($("FormatForm").LINE_LENGTH); + + + formatParams += getHiddenFieldParamString("BUILD_NAME"); + + var serviceType = ""; + if ($("serviceType").value == "sra") { + serviceType = "sra"; + } + else if ($("clientType").value == "TMSmart_restricted") { + serviceType = "restricted"; + } + if (serviceType != "") { + formatParams += "&BOBJSRVC=" + serviceType; + } + if ($("currQuery").value != "") { + formatParams += "&CURR_QUERY_ID=" + $("currQuery").value; + } + + return formatParams; +} + +//readAln.seqList contains one gi only for this +function SendReadSeqAlinSortHSPRequest(readAln) { + blastUrl = "t2g.cgi"; + var rp = new RemoteDataProvider(blastUrl); + + + rp.onSuccess = function(obj) { + var moreHspsLink = (readAln.hasOwnProperty("AlignDbPageNum")) ? getNextHspsLink(readAln) : ""; + var alnHtml = obj.responseText + moreHspsLink; + initHSPRequest(readAln, obj.responseText + moreHspsLink,false); + if (readAln.scrollToSeqID) { + location.href = "#" + readAln.scrollToSeqID; + } + }; + rp.onError = function(obj) { + var currHspInd = (readAln.hasOwnProperty("AlignDbPageNum")) ? readAln.AlignDbPageSize * readAln.AlignDbPageNum : 0; + var msgID = "erm_" + readAln.gi + "_" + (currHspInd + 1); + if (!$(msgID)) { + var msg = "
"; + initHSPRequest(readAln, msg, true); + } + else { + var attNum = parseInt($(msgID).getAttribute("att")) + 1; + $(msgID).setAttribute("att", attNum); + jQuery($(msgID)).find(".attmt").each(function(index) { + jQuery(this).html(", attempt " + attNum); + }); + } + } + + var params = constructURLParams(readAln); + if (readAln.AlignDbPageSize) { + params += "&TOTAL_HSPS=" + $("deflnDesc_" + readAln.startIndex).getAttribute("hsp"); + } + params += "&SORT_ONE_ALN=on"; + var formatParams = constructFormatParams(); + + params += formatParams; + + //alert(params); + rp.Request(params); +} +function initHSPRequest(readAln, alnHtml, err) { + var currHspInd = (readAln.hasOwnProperty("AlignDbPageNum")) ? readAln.AlignDbPageSize * readAln.AlignDbPageNum : 0; + if (currHspInd != 0) { + readAln.insertAfterID = "ar_" + readAln.gi + "_" + currHspInd; + jQuery($(readAln.insertAfterID)).after(alnHtml); + moreHspsID = "nxHsp" + readAln.gi + "_" + (currHspInd + 1); + jQuery($(moreHspsID)).remove(); + if (!err) { + errMsgID = "erm_" + readAln.gi + "_" + (currHspInd + 1); + jQuery($(errMsgID)).remove(); + } + } + else { + jQuery($("alnAll_" + readAln.gi)).html(alnHtml); + } +} + +function SortHSPAlnSel(e, sortLink) {//example id="sa_207524544" + var readAln = new Object(); + + + var desLineID = sortLink.id.replace("sa", "dtr"); //tr id + var seqInd; + + jQuery($($(desLineID))).find(".deflnDesc").each(function(index) { + seqInd = this.getAttribute("ind"); + }); + + ReadNextHSPSet(parseInt(seqInd), 0); +} + + +function configDescriptions(e,btn,dlgId) +{ + var suffix = PsiBelowThresh(dlgId); + var colmnsInfId = "cfcDsInf" + suffix; + var tblID = "dscTable" + suffix; //"dscTable[_psiw]" + var showAllColId = "shcl" + suffix; + var chkBoxes = $C("checkbox", "type", $(dlgId), "input"); + if (!utils.hasClass(btn, "cnc")) $(colmnsInfId).value = ""; + for (i = 0; i < chkBoxes.length; i++) { + var check; + if (utils.hasClass(btn, "cnc")) {//cancel + if ($(colmnsInfId).value.indexOf(chkBoxes[i].value) != -1 && !chkBoxes[i].checked) { + check = true; + } + else if ($(colmnsInfId).value.indexOf(chkBoxes[i].value) == -1 && chkBoxes[i].checked) { + check = false; + } + } + else if (utils.hasClass(btn, "rdf") && !chkBoxes[i].checked) { + check = true; + } + if (typeof (check) != 'undefined') { + chkBoxes[i].checked = check; + showHideCol(tblID,parseInt(chkBoxes[i].value), !check); + } + if (!utils.hasClass(btn, "cnc")) { + if (chkBoxes[i].checked) { //OK + if ($(colmnsInfId).value != "") $(colmnsInfId).value += ","; + $(colmnsInfId).value += chkBoxes[i].value; + } + } + } + if ($(colmnsInfId).value != $(colmnsInfId).getAttribute("defval")) {//defval = "2,3,4,5,6,7,8" + jQuery($(showAllColId)).removeClass("hidden"); + } + else { + jQuery($(showAllColId)).addClass("hidden"); + } + + var chConfig = $("cfcDsSave").value != $(colmnsInfId).value; + + var cfds = document.getElementsByName("CONFIG_DESCR"); + if (cfds) { + for (i = 0; i < cfds.length; i++) { + cfds[i].value = $(colmnsInfId).value; + } + } + $("cfcDsSave").value = $(colmnsInfId).value; + if (chConfig) SaveConfigTable(); + jQuery(document.body).click(); + utils.preventDefault(e); +} + + + +function initDescConfig() +{ + initConfigColumns("dsConfig"); + if ($("psiw") && utils.hasClass($("psiw"), "shown")) { + initConfigColumns("dsConfig_psiw"); + } +} + + +function initConfigColumns(cnfDlgID) +{ + var suffix = PsiBelowThresh(cnfDlgID); + //cnfDlgID is "dsConfig[_psiw]" + var colmnsInfId = "cfcDsInf" + suffix; + var tblID = "dscTable" + suffix; //"dscTable[_psiw]" + var showAllColId = "shcl" + suffix; + + if (navigator.userAgent.match(/ie/i)) { + if ($("FormatForm").NCBI_GI.checked || $("serviceType").value == "sra") { + jQuery($(tblID)).find("th.c1").each(function(index) { + db = getHiddenFieldVal("DATABASE"); + var width = (db.match(/WGS/i) || db.match(/Whole_Genome_Shotgun_contigs/i)) ? "16em" : "14em"; + jQuery(this).css("width", width); + }); + } + } + + jQuery($(tblID)).find("tr.first").each(function(index) { + jQuery(this).find("a.dcs").each(function(index) { + jQuery(this).bind("click", function(e) { checkConfig(this); }); + }); + }); + + jQuery($(cnfDlgID)).find("button").each(function(index) { + jQuery(this).bind("click", function(e) { configDescriptions(e, this, cnfDlgID); }); + }); + + + jQuery($(cnfDlgID)).bind("click", function(e) { e.stopPropagation(); }); + + $(colmnsInfId).value = getHiddenFieldVal("CONFIG_DESCR"); + if ($(colmnsInfId).value == "" || $(colmnsInfId).value == "undefined") { + $(colmnsInfId).value = $(colmnsInfId).getAttribute("defval"); + } + if ($(colmnsInfId).value != $(colmnsInfId).getAttribute("defval")) {//defval = "2,3,4,5,6,7,8" + jQuery($(showAllColId)).removeClass("hidden"); + } + else { + jQuery($(showAllColId)).addClass("hidden"); + } + var chkBoxes = $C("checkbox", "type", $(cnfDlgID), "input") + for (i = 0; i < chkBoxes.length; i++) { + jQuery(chkBoxes[i]).bind("click", configColumn); + if ($(colmnsInfId).value.indexOf(chkBoxes[i].value) != -1) { + chkBoxes[i].checked = true; + } + else { + //jQuery($(tblID)).ncbigrid("hideColumn", chkBoxes[i].value); + showHideCol($(tblID), chkBoxes[i].value, true); + } + } +} +function showAllCol(e,elem) +{ + var suffix = PsiBelowThresh(elem.id); + var rdf = "dscRsDf" + suffix; + jQuery($(rdf)).click();//click "restore defaults' + utils.preventDefault(e); +} + + +function configColumn() { + var suffix = PsiBelowThresh(this.id); + var tblID = "dscTable" + suffix; //"dscTable[_psiw]" + + cCls = "c" + this.value; + if (this.checked) {//show + showHideCol(tblID,parseInt(this.value), false); + } + else { + showHideCol(tblID,parseInt(this.value), true); + } +} + +function showHideCol(tblID, columnIndex, hide) { + + if ($("Transcr")) { + colHidden = utils.hasClass($("c" + columnIndex), "ui-ncbigrid-column-hidden"); + hide = hide && !colHidden; + show = !hide && colHidden; + } + else { + show = !hide; + } + if (hide) { + jQuery($(tblID)).ncbigrid("hideColumn", columnIndex); + } + else if (show) { + jQuery($(tblID)).ncbigrid("showColumn", columnIndex); + } + if ($("Transcr") && (hide || show) ) { + var colsp = parseInt($("Transcr").getAttribute("colspan")); + colsp = (hide) ? colsp - 1 : colsp + 1; + $("Transcr").setAttribute("colSpan", colsp); + if ($("GnmSeq")) $("GnmSeq").setAttribute("colSpan", colsp); + } +} + +function checkConfig(lnk) { + var cnfCol = "&CONFIG_DESCR=" + $("cfcDsSave").value; + lnk.href = lnk.href + cnfCol + "#sort_mark"; +} + +function DisplayAlignFromGraphics(seqID,e) //SeqID = gi if exists +{ + var dflLineLinks = $C(seqID, "gi", document, "a"); + for (i = 0; i < dflLineLinks.length; i++) { + jQuery(dflLineLinks[i]).click(); + break; + } + location.href = dflLineLinks[i].href; +} + + + +function initDescSelect() +{ + + jQuery("#cntDesc").find("a").each(function(index) { + jQuery(this).bind("click", configDescrSelect); + }); + jQuery("#cntSelN").click(); + jQuery("#descTblCtrl").find("a[view]").each(function(index) { + jQuery(this).bind("click", DisplaySelectedView); + }); + if ($("psiw") && utils.hasClass($("psiw"), "shown")) { + jQuery("#cntDesc_psiw").find("a").each(function(index) { + jQuery(this).bind("click", configDescrSelect); + }); + jQuery("#cntSelN_psiw").click(); + jQuery("#descTblCtrl_psiw").find("a[view]").each(function(index) { + jQuery(this).bind("click", DisplaySelectedView); + }); + } + + + //jQuery("#dsConfig").bind("click", function(e) { e.stopPropagation(); });?? + +} + +function DisplaySelectedView(e) { + if (this.getAttribute("view") == "graph") { //seqviewer + ViewSelectedSeqViewer(e,this); + } + else { + if (this.getAttribute("view") == "tree") { //seqviewer + $("scrWidth").value = screen.width; + $("scrHeight").value = screen.height; + } + ViewSelectedSeqsEx(e, this); + } +} + +function PsiBelowThresh(elemID) +{ + var suffix = ""; + if (elemID.indexOf("_psiw") != -1) { + suffix = "_psiw"; + } + return suffix; +} + +function ViewSelectedSeqsEx(e,elem) { + var sbmForm = elem.getAttribute("frm"); + var seqList = elem.getAttribute("seqList"); + + var cnfElem = utils.getParent(elem); //.cnf div + var suffix = PsiBelowThresh(cnfElem.id); + var tblID = "dscTable" + suffix; + + $(seqList).value = createSelseqString(tblID,true); + $(seqList).value = $(seqList).value.replace(/ti:/g, ""); //For traces + if ($(seqList).value.indexOf("dbSNP") != -1) { + $(seqList).value = $(seqList).value.replace(/dbSNP:rs/g, ""); //For snp + elem.href = $(sbmForm).action + $(seqList).value; + elem.target = "new"; + } + else { + $(sbmForm).submit(); + utils.preventDefault(e); + } +} + +function ViewSelectedSeqsTree(e) { + $("scrWidth").value = screen.width; + $("scrHeight").value = screen.height; +} + +function initSeqViewerGet(seqList) { + if (seqList.length >= 2000) { + seqList = seqList.substr(0,2000); + lastComma = seqList.lastIndexOf(","); + seqList = seqList.substr(0,lastComma); + } + $("seqViewParams").name = "RID"; + $("seqViewParams").value = $("ridParam").value + "[" + seqList + "]"; +} + +function ViewSelectedSeqViewer(e, elem) +{ + var cnfElem = utils.getParent(elem); //.cnf div + var suffix = PsiBelowThresh(cnfElem.id); + var tblID = "dscTable" + suffix; + + //change to false when new verison of seqVier is installed in production + var seqList = createSelseqString(tblID, false); + $("sbmtGraphics").action = $("seqViewUrl").value; + + var rp = new RemoteDataProvider("url2nc.cgi"); + rp.onSuccess = function(obj) { + var jsnResp = JSON.parse(obj.responseText); + ncid = jsnResp.ncid; + + if (ncid != "") { + $("seqViewParams").name = "rkey"; + $("seqViewParams").value = ncid; + } + else { + initSeqViewerGet(seqList); + } + $("sbmtGraphics").submit(); + }; + rp.onError = function(obj) { + initSeqViewerGet(seqList); + $("sbmtGraphics").submit(); + utils.preventDefault(e); + } + var params = $("ridParam").value + "[" + seqList + "]"; + rp.Request(params, "POST"); + utils.preventDefault(e); +} + +function configDescrSelect(e) { + var sel = this.getAttribute("sel"); + if (sel) { + var selNum = 0; + var check = (sel == "all") ? true : false; + + var suffix = PsiBelowThresh(this.id); + var tblID = "dscTable" + suffix; + var toolbarID = "descTblCtrl" + suffix; + var selElID = "slcNum" + suffix; + + jQuery($(tblID)).find("input[type='checkbox'].cb").each(function(index) { + jQuery(this)[0].checked = check; + if (check) selNum++; + }); + enableDescrLinks(selNum, toolbarID, selElID); + } + utils.preventDefault(e); +} + + + +function enableDescrLinks(selNum, toolbarID, selElID) { + jQuery($(toolbarID)).find("a[minSlct]").each(function(index) { + var minSelected = this.getAttribute("minSlct"); + minSelected = parseInt(minSelected); + if (selNum >= minSelected) { + this.removeAttribute("disabled"); + } + else { + this.setAttribute("disabled", "disabled"); + } + }); + $(selElID).innerHTML = selNum; +} + + + +function configDescrLinks(e, elem) +{ + + ncbi.sg.ping(elem, "click", elem.checked ? "checked=true" : "checked=false"); + var par = jQuery(elem).parents(".jig-ncbigrid");//parent table + if (par) { + var suffix = PsiBelowThresh(par[0].id); + var tblID = "dscTable" + suffix; + var toolbarID = "descTblCtrl" + suffix; + var selElID = "slcNum" + suffix; + + var currSelNum = parseInt($(selElID).innerHTML); + var selNum = elem.checked ? currSelNum + 1 : currSelNum - 1; + enableDescrLinks(selNum, toolbarID, selElID); + } +} +/***Download code begin****/ + +function initDownLoadPopup(dwnDialog) { + + jQuery(dwnDialog).find("button").each(function(index) { + jQuery(this).bind("click", execDownLoad); + }); + + jQuery(dwnDialog).bind("click", function(e) { e.stopPropagation(); }); +} + +function initDescDownLoad() { + initDownLoadPopup($("dsDownload")); + + if ($("psiw") && utils.hasClass($("psiw"), "shown")) { + initDownLoadPopup($("dsDownload_psiw")); + } +} + +function initAlignDownLoad(navObj) +{ + var seqID = navObj.seqID; + var dwnDialog = $("dlgDwnl_" + seqID); + jQuery(dwnDialog).find("button").each(function(index) { + jQuery(this).bind("click", execDownLoad); + }); + + var dwnFSTW = $("dwFST_" + seqID);//whole seq + var dwnFSTAl = $("dwFSTAl_" + seqID);//aligned regions + + if(dwnFSTW) dwnFSTW.setAttribute("seqfsta", navObj.currSeqID); + if(dwnFSTAl) dwnFSTAl.setAttribute("seqfsta", navObj.currSeqID); + + jQuery(dwnDialog).bind("click", function(e) { e.stopPropagation(); }); +} + + +function execDownLoad(e) { + if (!utils.hasClass(this, "cnc")) { + par = utils.getParent(this); + dwnDialog = utils.getParent(par); //parent dialog with popDl class + var descr = (this.id == "dw_cont" || this.id == "dw_cont_psiw") ? true : false; + jQuery(dwnDialog).find("input").each(function(index) { + if (this.checked) { + submitDownLoad(this, descr); + } + }); + } + jQuery(document.body).click(); + utils.preventDefault(e); +} + +function submitDownLoad(radioElem, descr) { + var toolURL = radioElem.getAttribute("url"); + if (toolURL) { + if (descr) { + var getGi = radioElem.getAttribute("getGi"); + getGi = (getGi) ? true : false; + + var tblID = "dscTable"; + var suffix = PsiBelowThresh(radioElem.id); + tblID += suffix; + + $("selDnSeqs").value = createSelseqString(tblID,getGi); + } + else { + var seqfsta = radioElem.getAttribute("seqfsta"); + $("selDnSeqs").value = (seqfsta) ? seqfsta : radioElem.getAttribute("getGi"); + } + var addParams = ""; + if (radioElem.getAttribute("addParam")) { + addParams = addDwnlParams(); + } + var submitName = radioElem.getAttribute("sbName") + $("selDnSeqs").name = (submitName) ? submitName : "ALIGN_SEQ_LIST"; + $("dwdlSubmit").action = toolURL + addParams; + $("dwdlSubmit").submit(); + } + else { + var sbFunction = radioElem.getAttribute("sbFunc"); + if (sbFunction) { + eval(sbFunction + "(radioElem, descr)"); + } + } +} + + +function initDownLoadFSTA(radioElem, descr) +{ + if (descr) { + + var tblID = "dscTable"; + var suffix = PsiBelowThresh(radioElem.id); + tblID += suffix; + + $("sbmtFASTA").ALIGN_SEQ_LIST.value = createSelseqString(tblID,false); + } + else { + $("sbmtFASTA").ALIGN_SEQ_LIST.value = radioElem.getAttribute("seqfsta"); + } + $("sbmtFASTA").DOWNLOAD_TYPE.value = radioElem.getAttribute("fstaDWType"); + + $("sbmtFASTA").DATABASE.value = getHiddenFieldVal("DATABASE"); + if ($("useAlignDB") && $("useAlignDB").value == "true") {//temp checkbox + var batchID = document.getElementsByName("ALIGNDB_BATCH_ID"); + if (batchID) { + $("sbmtFASTA").ALIGNDB_BATCH_ID.value = getHiddenFieldVal("ALIGNDB_BATCH_ID"); + $("sbmtFASTA").ALIGNDB_MASTER_ALIAS.value = getHiddenFieldVal("ALIGNDB_MASTER_ALIAS"); + $("sbmtFASTA").ALIGNDB_CGI_HOST.value = getHiddenFieldVal("ALIGNDB_CGI_HOST"); + $("sbmtFASTA").ALIGNDB_CGI_PATH.value = getHiddenFieldVal("ALIGNDB_CGI_PATH"); + } + } + $("sbmtFASTA").submit(); +} + +function createSelseqString(tblID,getGi) { + var selSeqs = ""; + jQuery($(tblID)).find("input[type='checkbox'].cb").each(function(index) { + if (jQuery(this)[0].checked) { + if (selSeqs != "") selSeqs += ","; + if (getGi) { + selSeqs += jQuery(this)[0].value; + } + else { + var linkID = jQuery(this)[0].id.replace("chk", "deflnDesc"); + selSeqs += $(linkID).getAttribute("seqFSTA"); + } + } + }); + return selSeqs; +} + +/***Download code end****/ + +/***Init navigation code begin **/ + +function initNavigation(navObj) { + initNextAlnLink(navObj, true); + initNextAlnLink(navObj, false); +} + + +function initNavInfo(navObj) { + var currInd = parseInt($("dtr_" + navObj.seqID).getAttribute("ind")); + nextInd = currInd + 1; + prevInd = currInd - 1; + + navObj.currSeqID = ""; + navObj.nextSeqID = ""; + navObj.prevSeqID = ""; + + if ($("deflnDesc_" + nextInd)) { + navObj.nextSeqID = $("deflnDesc_" + nextInd).getAttribute("accs"); + if(navObj.nextSeqID =="") navObj.nextSeqID = $("deflnDesc_" + nextInd).getAttribute("seqFSTA"); + } + if ($("deflnDesc_" + prevInd)) { + navObj.prevSeqID = $("deflnDesc_" + prevInd).getAttribute("accs"); + if (navObj.prevSeqID == "") navObj.prevSeqID = $("deflnDesc_" + prevInd).getAttribute("seqFSTA"); + } + if ($("deflnDesc_" + currInd)) { + navObj.currSeqID = $("deflnDesc_" + currInd).getAttribute("seqFSTA"); + } +} + + +function initNextAlnLink(navObj, next) { + + var nextLinkEl = (next) ? $("alnNxt_" + navObj.seqID) : $("alnPrv_" + navObj.seqID); + var nextSeqid = (next) ? navObj.nextSeqID : navObj.prevSeqID; + + if (nextLinkEl) { + if (nextSeqid != "") { + var text = (next) ? "next" : "previous"; + nextLinkEl.setAttribute("title", "Go to " + text + " alignment for " + nextSeqid); + } + else { + nextLinkEl.setAttribute("disabled", "disabled"); + } + } +} +function scan(link) { + var init = link.getAttribute("init"); + if (!init) { + ncbi.sg.scanLinks(link); + link.setAttribute("init","on"); + } +} + +function initWidth(seqID) { + var lineLengthElem = $("FormatForm").LINE_LENGTH; + var lineLength = parseInt(lineLengthElem[lineLengthElem.selectedIndex].value); + if (parseInt(lineLengthElem.getAttribute("defval")) == lineLength) return; + + var relWidth = (lineLength > 90) ? "12%" : "15%"; + var charWidth = (navigator.userAgent.match(/ie/i)) ? 8 : 7; + lineLength = (lineLength + parseInt(17)) * charWidth; + var width = lineLength + "px"; + jQuery($("alnAll_" + seqID)).find("div.dflLnk").each(function(index) { + jQuery(this).css("width", width); + }); + jQuery($("alnAll_" + seqID)).find("table.alnParams").each(function(index) { + jQuery(this).css("width", width); + }); + jQuery($("relInf_" + seqID)).css("width", relWidth); +} + + +/***Init navigation code end **/ +function initAlignBatch(seqID) +{ + var navObj = new Object(); + navObj.seqID = seqID; + initNavInfo(navObj); + + initAlignDownLoad(navObj); + initNavigation(navObj); + ncbi.sg.scanLinks($("alnNxt_" + seqID)); + ncbi.sg.scanLinks($("alnPrv_" + seqID)); + if ($("serviceType").value == "vecscreen") { + utils.addClass($("alnDsc_" + seqID), "hidden"); + } + ncbi.sg.scanLinks($("alnDwnld_" + seqID)); + jQuery($("csLinks_" + seqID)).find("a").each(function(index) { + ncbi.sg.scanLinks(this); + }); + jQuery($("relInf_" + seqID)).find("a").each(function(index) { + ncbi.sg.scanLinks(this); + }); + jQuery($("rng_" + seqID)).find("a").each(function(index) { + ncbi.sg.scanLinks(this); + }); + jQuery($("dln_" + seqID)).find("a").each(function(index) { + ncbi.sg.scanLinks(this); + }); + initWidth(seqID); +/* + jQuery($("alnHdr_" + seqID)).find("a").each(function(index) { + ncbi.sg.scanLinks(this); + }); + jQuery($("aln_" + seqID)).find("a").each(function(index) { + ncbi.sg.scanLinks(this); + }); +*/ +} + +function SaveConfigTable() { + blastUrl = "fmtsave.cgi"; + + + var rp = new RemoteDataProvider(blastUrl); + + + rp.onSuccess = function(obj) { + //alert("success"); + }; + rp.onError = function(obj) { + //alert("error"); + } + + var program = getHiddenFieldVal("PROGRAM"); + var rid = getHiddenFieldVal("RID"); + var blastSpec = getHiddenFieldVal("BLAST_SPEC"); + var params = "CMD=Get&RID=" + rid + "&ViewReport=on&PROGRAM=" + program + "&SAVE_INDV_FRM_OPTION=on&CONFIG_DESCR=" + $("cfcDsSave").value; + if(blastSpec) { + params += "&BLAST_SPEC=" + blastSpec; + } + rp.Request(params,"POST"); +} + +function removeRID() { + var rid = document.getElementsByName("RID"); + for (var i = 0; i <= rid.length; i++) { + jQuery(rid[i]).remove(); + } +} + +function initAdvancedView() +{ + if ($("dsConfig")) { + + var alnView = getHiddenFieldVal("ALIGNMENT_VIEW"); + if (alnView == "Pairwise" || alnView == "PairwiseWithIdentities") { + var rid = getHiddenFieldVal("RID"); + ReadNextSeqAligns(0, 5); + g_alignViewPos = $("alignView").getBoundingClientRect().top; + utils.addEvent(window, "scroll", checkAutoAlignLoad, false); + } + list = $("phiPtInd"); + if (list) { + utils.addEvent(list, "change", GetPatternLocResults, false); + } + initDescConfig(); + initDescSelect(); + initDescDownLoad(); + if ($("psiInp")) { + var nextIter = document.getElementsByName("NEXT_I"); + for (var i = 0; i < nextIter.length; i++) { + utils.addEvent(nextIter[i], "click", removeRID, false); + } + } + } +} + +//takes care of jQuery calls to elements that have dots in id like id= "SRA34456.3.4" +function initjQry() +{ + var oldCreate = jQuery.ui.ncbipopper.prototype._create; + jQuery.ui.ncbipopper.prototype._create = function() { + var destSelector = this.options.destSelector || this.options.sourceSelector || this.element.prop("hash"); + this.options.destSelector = destSelector.replace(/\./g, "\\."); + oldCreate.apply(this, arguments); + } +} +utils.addEvent(window, + "load", initAdvancedView, + false); + +initjQry() + +/* If user agent has "safari" in it, include safari-specific stylesheet. */ +if (navigator.userAgent.match(/ie/i)) { + document.write(""); +} +/*****************************new code end*********************************************************************/ diff -r 000000000000 -r a54279222d84 NCBI Blast reference example_files/helix.gif Binary file NCBI Blast reference example_files/helix.gif has changed diff -r 000000000000 -r a54279222d84 NCBI Blast reference example_files/jig.css --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NCBI Blast reference example_files/jig.css Mon May 19 09:43:54 2014 -0400 @@ -0,0 +1,1 @@ +.ui-helper-hidden{display:none;}.ui-helper-hidden-accessible{position:absolute;left:-99999999px;}.ui-helper-reset{margin:0;padding:0;border:0;outline:0;line-height:1.3;text-decoration:none;font-size:100%;list-style:none;}.ui-helper-clearfix:after{content:".";display:block;height:0;clear:both;visibility:hidden;}.ui-helper-clearfix{display:inline-block;}/* required comment for clearfix to work in Opera \*/ * html .ui-helper-clearfix{height:1%;}.ui-helper-clearfix{display:block;}/* end clearfix */ .ui-helper-zfix{width:100%;height:100%;top:0;left:0;position:absolute;opacity:0;filter:Alpha(Opacity=0);}.ui-state-disabled{cursor:default!important;}.ui-icon{display:block;text-indent:-99999px;overflow:hidden;background-repeat:no-repeat;}.ui-widget-overlay{position:absolute;top:0;left:0;width:100%;height:100%;}.ui-widget{font-size:1.1em;}.ui-widget-content{border:1px solid #aaa;background:#fff url(images/ui-bg_flat_75_ffffff_40x100.png) 50% 50% repeat-x;color:#222;}.ui-widget-content a{color:#222;}.ui-widget-header{border:1px solid #aaa;background:#ccc url(images/ui-bg_highlight-soft_75_cccccc_1x100.png) 50% 50% repeat-x;color:#222;font-weight:bold;}.ui-widget-header a{color:#222;}.ui-state-default,.ui-widget-content .ui-state-default{border:1px solid #d3d3d3;background:#e6e6e6 url(images/ui-bg_glass_75_e6e6e6_1x400.png) 50% 50% repeat-x;font-weight:normal;color:#555;}.ui-state-default a,.ui-state-default a:link,.ui-state-default 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-224px;}.ui-corner-tl{-moz-border-radius-topleft:4px;-webkit-border-top-left-radius:4px;border-top-left-radius:4px;}.ui-corner-tr{-moz-border-radius-topright:4px;-webkit-border-top-right-radius:4px;border-top-right-radius:4px;}.ui-corner-bl{-moz-border-radius-bottomleft:4px;-webkit-border-bottom-left-radius:4px;border-bottom-left-radius:4px;}.ui-corner-br{-moz-border-radius-bottomright:4px;-webkit-border-bottom-right-radius:4px;border-bottom-right-radius:4px;}.ui-corner-top{-moz-border-radius-topleft:4px;-webkit-border-top-left-radius:4px;border-top-left-radius:4px;-moz-border-radius-topright:4px;-webkit-border-top-right-radius:4px;border-top-right-radius:4px;}.ui-corner-bottom{-moz-border-radius-bottomleft:4px;-webkit-border-bottom-left-radius:4px;border-bottom-left-radius:4px;-moz-border-radius-bottomright:4px;-webkit-border-bottom-right-radius:4px;border-bottom-right-radius:4px;}.ui-corner-right{-moz-border-radius-topright:4px;-webkit-border-top-right-radius:4px;border-top-right-radius:4px;-moz-border-radius-bottomright:4px;-webkit-border-bottom-right-radius:4px;border-bottom-right-radius:4px;}.ui-corner-left{-moz-border-radius-topleft:4px;-webkit-border-top-left-radius:4px;border-top-left-radius:4px;-moz-border-radius-bottomleft:4px;-webkit-border-bottom-left-radius:4px;border-bottom-left-radius:4px;}.ui-corner-all{-moz-border-radius:4px;-webkit-border-radius:4px;border-radius:4px;}.ui-widget-overlay{background:#aaa url(images/ui-bg_flat_0_aaaaaa_40x100.png) 50% 50% repeat-x;opacity:.30;filter:Alpha(Opacity=30);}.ui-widget-shadow{margin:-8px 0 0 -8px;padding:8px;background:#aaa url(images/ui-bg_flat_0_aaaaaa_40x100.png) 50% 50% repeat-x;opacity:.30;filter:Alpha(Opacity=30);-moz-border-radius:8px;-webkit-border-radius:8px;border-radius:8px;}.ui-widget{font-family:arial,"sans-serif"!important;font-size:100%;}.ui-helper-reset{font-size:100%!important;}iframe.ui-ncbi-iframe-fix{position:absolute;top:0;left:0;height:200px;z-index:3000;display:block;filter:alpha(opacity=1);}#ui-datepicker-div{display:none;}.ui-widget-content a{color:#2F4A8B;}.ui-helper-hidden-accessible{left:-10000000px!important;}#jig-ncbi_requires_login iframe{border:none;} \ No newline at end of file diff -r 000000000000 -r a54279222d84 NCBI Blast reference example_files/jig.js --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NCBI Blast reference example_files/jig.js Mon May 19 09:43:54 2014 -0400 @@ -0,0 +1,265 @@ +(function(){function Ka(){var g=null,j=jQuery.cookie("WebCubbyUser");if(j)if(j.indexOf("logged-in=true")>-1)if(j=j.match(/my-name=([^;]+)/i))g=j[1];return g}function W(g){this.name=this.selector="";this.onPage=false;this.dependsOn=[];this.interactions=[];this.overrideDefaults={};this.addCss=function(){document.write('')};this.addJs=function(){document.write(' + + + + + + +
+ +
+
This html page seems to have been stripped by Galaxy.
+ Disable Galaxy's html sanitization feature to view the full page (see sanitize_all_html in your galaxy's universe_wsgi.ini), or download this page instead of viewing it in Galaxy. +
+
+ +
+ + {% if not blast.BlastOutput_iterations.findall('Iteration') %} +
+

No data

+
+ No matches +
+
+ + {% else %} + + {% if blast.BlastOutput_iterations.findall('Iteration') | length > 1 %} +
+

Queries

+ + {% for result in blast.BlastOutput_iterations.Iteration %} +
+ {% endfor %} + +
+ {% endif %} + + {% for result in blast.BlastOutput_iterations.Iteration %} + +
+ +

Nucleotide Sequence ({{result|len}} letters)

+ +
+ + + {% for param, value in params %} + + {% endfor %} +
{{param}}:{{value}}
+ +
+ + {% set hits = result|hits %} + {% if not hits %} +
+

No Hits

+
+ + +
Message:{{result.Iteration_message}}
+
+
+ {% else %} + +
+

Graphic Summary

+ +
+

Distribution of {{result|length}} Blast Hits on the Query Sequence

+ +
+ Mouse-over to show defline and scores, click to show alignments +
+ +
+

Color key for alignment scores

+
+
<40
+
40–50
+
50–80
+
80–200
+
200≤
+
+
+ +
+ +
+
query:
+
+
+ {% for s in result|queryscale %} +
+ {% if s.width > 3.0 %} +
{{s.label}}
+ {% else %} +
 
+
{{s.label}}
+ {% endif %} +
+ {% endfor %} +
+
+
+
+ + {% for line in result|match_colors %} + +
+ {% for hit in line.colors %} +
+ {% endfor %} +
+
+ + {% endfor %} +
+
+
+
+ + + +
+

Descriptions

+ +
+

Sequences producing significant alignments:

+ + + + + + + + + + + + + {% for hit in result|hit_info %} + + + + + + + + + + {% endfor %} +
DescriptionMax scoreTotal scoreQuery coverE valueIdentAccession
{{hit.maxscore}}{{hit.totalscore}}{{hit.cover}}{{hit.e_value}}{{hit.ident}}{{hit.accession}}
+ +
+
+ + + +
+

Alignments

+ +
+ {% for hit in hits %} +
+ + + +
+

{{hit|firsttitle}}

+

+ Sequence ID: {{hit|seqid}} + Length: {{hit.Hit_len}} + Number of Matches: {{hit.Hit_hsps.Hsp|length}} +

+
+ + {% if hit|othertitles|length %} + + See {{hit|othertitles|length}} more title(s) + + + + {% endif %} + + {% for hsp in hit.Hit_hsps.Hsp %} +
+

+ Range {{hsp.Hsp_num}}: {{hsp['Hsp_hit-from']}} to {{hsp['Hsp_hit-to']}} + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
{{hsp['Hsp_bit-score']|fmt('.1f')}} bits({{hsp.Hsp_score}}){{hsp.Hsp_evalue|fmt('.1f')}}{{ hsp.Hsp_identity }}/{{ hsp|len }}({{ + (hsp.Hsp_identity/hsp|len) |fmt('.0%') }}){{ hsp.Hsp_gaps }}/{{ hsp|len + }}({{ (hsp.Hsp_gaps / hsp|len) | fmt('.0%') }}){{ hsp['Hsp_query-frame']|asframe }}/{{ hsp['Hsp_hit-frame']|asframe }}
+ +
{{hsp|alignment_pre}}
+
+ {% endfor %} + +
+ + {% endfor %} +
+
+ {% endif %} +
+ {% endfor %} + {% endif %} + +
+ + + + + +{# +Local Variables: +tab-width: 2 +indent-tabs-mode: nil +End: +#} diff -r 000000000000 -r a54279222d84 blast2html.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/blast2html.py Mon May 19 09:43:54 2014 -0400 @@ -0,0 +1,315 @@ +#!/usr/bin/env python3 +# Actually runs under either python 2 or 3 + +# Copyright The Hyve B.V. 2014 +# License: GPL version 3 or higher + +import sys +import math +import warnings +from os import path +from itertools import repeat +import argparse +from lxml import objectify +import jinja2 + + + +_filters = {} +def filter(func_or_name): + "Decorator to register a function as filter in the current jinja environment" + if isinstance(func_or_name, str): + def inner(func): + _filters[func_or_name] = func.__name__ + return func + return inner + else: + _filters[func_or_name.__name__] = func_or_name.__name__ + return func_or_name + + +def color_idx(length): + if length < 40: + return 0 + elif length < 50: + return 1 + elif length < 80: + return 2 + elif length < 200: + return 3 + return 4 + +@filter +def fmt(val, fmt): + return format(float(val), fmt) + +@filter +def firsttitle(hit): + return hit.Hit_def.text.split('>')[0] + +@filter +def othertitles(hit): + """Split a hit.Hit_def that contains multiple titles up, splitting out the hit ids from the titles.""" + id_titles = hit.Hit_def.text.split('>') + + titles = [] + for t in id_titles[1:]: + fullid, title = t.split(' ', 1) + hitid, id = fullid.split('|', 2)[1:3] + titles.append(dict(id = id, + hitid = hitid, + fullid = fullid, + title = title)) + return titles + +@filter +def hitid(hit): + hitid = hit.Hit_id.text + s = hitid.split('|', 2) + if len(s) >= 2: + return s[1] + return hitid + +@filter +def seqid(hit): + hitid = hit.Hit_id.text + s = hitid.split('|', 2) + if len(s) >= 3: + return s[2] + return hitid + + +@filter +def alignment_pre(hsp): + return ( + "Query {:>7s} {} {}\n".format(hsp['Hsp_query-from'].text, hsp.Hsp_qseq, hsp['Hsp_query-to']) + + " {:7s} {}\n".format('', hsp.Hsp_midline) + + "Subject{:>7s} {} {}".format(hsp['Hsp_hit-from'].text, hsp.Hsp_hseq, hsp['Hsp_hit-to']) + ) + +@filter('len') +def blastxml_len(node): + if node.tag == 'Hsp': + return int(node['Hsp_align-len']) + elif node.tag == 'Iteration': + return int(node['Iteration_query-len']) + raise Exception("Unknown XML node type: "+node.tag) + + +@filter +def asframe(frame): + if frame == 1: + return 'Plus' + elif frame == -1: + return 'Minus' + raise Exception("frame should be either +1 or -1") + +def genelink(hit, type='genbank', hsp=None): + if not isinstance(hit, str): + hit = hitid(hit) + link = "http://www.ncbi.nlm.nih.gov/nucleotide/{}?report={}&log$=nuclalign".format(hit, type) + if hsp != None: + link += "&from={}&to={}".format(hsp['Hsp_hit-from'], hsp['Hsp_hit-to']) + return link + + +# javascript escape filter based on Django's, from https://github.com/dsissitka/khan-website/blob/master/templatefilters.py#L112-139 +# I've removed the html escapes, since html escaping is already being performed by the template engine. + +_base_js_escapes = ( + ('\\', r'\u005C'), + ('\'', r'\u0027'), + ('"', r'\u0022'), + # ('>', r'\u003E'), + # ('<', r'\u003C'), + # ('&', r'\u0026'), + # ('=', r'\u003D'), + # ('-', r'\u002D'), + # (';', r'\u003B'), + # (u'\u2028', r'\u2028'), + # (u'\u2029', r'\u2029') +) + +# Escape every ASCII character with a value less than 32. This is +# needed a.o. to prevent html parsers from jumping out of javascript +# parsing mode. +_js_escapes = (_base_js_escapes + + tuple(('%c' % z, '\\u%04X' % z) for z in range(32))) + +@filter +def js_string_escape(value): + """Escape javascript string literal escapes. Note that this only works + within javascript string literals, not in general javascript + snippets.""" + + value = str(value) + + for bad, good in _js_escapes: + value = value.replace(bad, good) + + return value + +@filter +def hits(result): + # sort hits by longest hotspot first + return sorted(result.Iteration_hits.findall('Hit'), + key=lambda h: max(blastxml_len(hsp) for hsp in h.Hit_hsps.Hsp), + reverse=True) + + + +class BlastVisualize: + + colors = ('black', 'blue', 'green', 'magenta', 'red') + + max_scale_labels = 10 + + def __init__(self, input, templatedir, templatename): + self.input = input + self.templatename = templatename + + self.blast = objectify.parse(self.input).getroot() + self.loader = jinja2.FileSystemLoader(searchpath=templatedir) + self.environment = jinja2.Environment(loader=self.loader, + lstrip_blocks=True, trim_blocks=True, autoescape=True) + + self._addfilters(self.environment) + + + def _addfilters(self, environment): + for filtername, funcname in _filters.items(): + try: + environment.filters[filtername] = getattr(self, funcname) + except AttributeError: + environment.filters[filtername] = globals()[funcname] + + def render(self, output): + template = self.environment.get_template(self.templatename) + + params = (('Query ID', self.blast["BlastOutput_query-ID"]), + ('Query definition', self.blast["BlastOutput_query-def"]), + ('Query length', self.blast["BlastOutput_query-len"]), + ('Program', self.blast.BlastOutput_version), + ('Database', self.blast.BlastOutput_db), + ) + + output.write(template.render(blast=self.blast, + iterations=self.blast.BlastOutput_iterations.Iteration, + colors=self.colors, + # match_colors=self.match_colors(), + # hit_info=self.hit_info(), + genelink=genelink, + params=params)) + + @filter + def match_colors(self, result): + """ + An iterator that yields lists of length-color pairs. + """ + + query_length = blastxml_len(result) + + percent_multiplier = 100 / query_length + + for hit in hits(result): + # sort hotspots from short to long, so we can overwrite index colors of + # short matches with those of long ones. + hotspots = sorted(hit.Hit_hsps.Hsp, key=lambda hsp: blastxml_len(hsp)) + table = bytearray([255]) * query_length + for hsp in hotspots: + frm = hsp['Hsp_query-from'] - 1 + to = int(hsp['Hsp_query-to']) + table[frm:to] = repeat(color_idx(blastxml_len(hsp)), to - frm) + + matches = [] + last = table[0] + count = 0 + for i in range(query_length): + if table[i] == last: + count += 1 + continue + matches.append((count * percent_multiplier, self.colors[last] if last != 255 else 'transparent')) + last = table[i] + count = 1 + matches.append((count * percent_multiplier, self.colors[last] if last != 255 else 'transparent')) + + yield dict(colors=matches, link="#hit"+hit.Hit_num.text, defline=firsttitle(hit)) + + @filter + def queryscale(self, result): + query_length = blastxml_len(result) + skip = math.ceil(query_length / self.max_scale_labels) + percent_multiplier = 100 / query_length + for i in range(1, query_length+1): + if i % skip == 0: + yield dict(label = i, width = skip * percent_multiplier) + if query_length % skip != 0: + yield dict(label = query_length, + width = (query_length % skip) * percent_multiplier) + + @filter + def hit_info(self, result): + + query_length = blastxml_len(result) + + for hit in hits(result): + hsps = hit.Hit_hsps.Hsp + + cover = [False] * query_length + for hsp in hsps: + cover[hsp['Hsp_query-from']-1 : int(hsp['Hsp_query-to'])] = repeat(True, blastxml_len(hsp)) + cover_count = cover.count(True) + + def hsp_val(path): + return (float(hsp[path]) for hsp in hsps) + + yield dict(hit = hit, + title = firsttitle(hit), + link_id = hit.Hit_num, + maxscore = "{:.1f}".format(max(hsp_val('Hsp_bit-score'))), + totalscore = "{:.1f}".format(sum(hsp_val('Hsp_bit-score'))), + cover = "{:.0%}".format(cover_count / query_length), + e_value = "{:.4g}".format(min(hsp_val('Hsp_evalue'))), + # FIXME: is this the correct formula vv? + ident = "{:.0%}".format(float(min(hsp.Hsp_identity / blastxml_len(hsp) for hsp in hsps))), + accession = hit.Hit_accession) + + +def main(): + default_template = path.join(path.dirname(__file__), 'blast2html.html.jinja') + + parser = argparse.ArgumentParser(description="Convert a BLAST XML result into a nicely readable html page", + usage="{} [-i] INPUT [-o OUTPUT]".format(sys.argv[0])) + input_group = parser.add_mutually_exclusive_group(required=True) + input_group.add_argument('positional_arg', metavar='INPUT', nargs='?', type=argparse.FileType(mode='r'), + help='The input Blast XML file, same as -i/--input') + input_group.add_argument('-i', '--input', type=argparse.FileType(mode='r'), + help='The input Blast XML file') + parser.add_argument('-o', '--output', type=argparse.FileType(mode='w'), default=sys.stdout, + help='The output html file') + # We just want the file name here, so jinja can open the file + # itself. But it is easier to just use a FileType so argparse can + # handle the errors. This introduces a small race condition when + # jinja later tries to re-open the template file, but we don't + # care too much. + parser.add_argument('--template', type=argparse.FileType(mode='r'), default=default_template, + help='The template file to use. Defaults to blast_html.html.jinja') + + args = parser.parse_args() + if args.input == None: + args.input = args.positional_arg + if args.input == None: + parser.error('no input specified') + + templatedir, templatename = path.split(args.template.name) + args.template.close() + if not templatedir: + templatedir = '.' + + b = BlastVisualize(args.input, templatedir, templatename) + b.render(args.output) + + +if __name__ == '__main__': + main() + diff -r 000000000000 -r a54279222d84 blast2html.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/blast2html.xml Mon May 19 09:43:54 2014 -0400 @@ -0,0 +1,44 @@ + + + Convert BLAST XML to HTML + + + jinja2 + lxml + argparse + + + blast2html.py -i "${input}" -o "${output}" + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + This tool converts the default BLAST XML result into a HTML document + + + diff -r 000000000000 -r a54279222d84 test-data/blast xml example1.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/blast xml example1.html Mon May 19 09:43:54 2014 -0400 @@ -0,0 +1,13220 @@ + + + + + + + Blast output + + + + + + + + + + +
+ +
+
This html page seems to have been stripped by Galaxy.
+ Disable Galaxy's html sanitization feature to view the full page (see sanitize_all_html in your galaxy's universe_wsgi.ini), or download this page instead of viewing it in Galaxy. +
+
+ +
+ + + + +
+ +

Nucleotide Sequence (16 letters)

+ +
+ + + + + + + +
Query ID:106397
Query definition:No definition line
Query length:16
Program:BLASTN 2.2.29+
Database:pdb
+ +
+ + +
+

Graphic Summary

+ +
+

Distribution of 1 Blast Hits on the Query Sequence

+ +
+ Mouse-over to show defline and scores, click to show alignments +
+ +
+

Color key for alignment scores

+
+
<40
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+

Descriptions

+ +
+

Sequences producing significant alignments:

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
DescriptionMax scoreTotal scoreQuery coverE valueIdentAccession
32.277.3100%0.0007913100%3J5K_A
32.277.3100%0.0007913100%3J5I_A
32.277.3100%0.0007913100%3J5G_A
32.277.3100%0.0007913100%3J5E_A
32.277.3100%0.0007913100%3J5C_A
32.277.3100%0.0007913100%3J5A_A
32.277.3100%0.0007913100%3J58_A
32.277.3100%0.0007913100%3J56_A
32.277.3100%0.0007913100%3J54_A
32.277.3100%0.0007913100%3J52_A
32.277.3100%0.0007913100%3J51_A
32.277.3100%0.0007913100%3J50_A
32.277.3100%0.0007913100%3J4X_A
32.262.9100%0.0007913100%3J37_A
32.262.9100%0.0007913100%3IZT_B
32.277.3100%0.0007913100%3FIK_B
32.277.3100%0.0007913100%3E1B_B
32.277.3100%0.0007913100%2GYC_0
32.277.3100%0.0007913100%2GYA_0
32.277.3100%0.0007913100%2I2V_B
32.277.3100%0.0007913100%2AW4_B
32.277.3100%0.0007913100%2AWB_B
32.277.3100%0.0007913100%1VS6_B
32.277.3100%0.0007913100%1P85_0
26.340.681%0.04882100%1C2W_B
18.336.781%11.992%3J44_1
18.336.781%11.992%3J2L_1
18.377.888%11.9100%3J62_AA
18.318.356%11.9100%4CE4_A
18.379.881%11.9100%4BYP_5
18.379.881%11.9100%4BYW_5
18.351.075%11.9100%4HUB_0
18.3128.8100%11.9100%3J3F_5
18.363.4100%11.9100%3J3E_5
18.332.781%11.9100%3ZEX_B
18.332.756%11.9100%3OW2_0
18.351.075%11.9100%4ADX_0
18.347.188%11.9100%3U5F_6
18.347.188%11.9100%3U5B_2
18.351.075%11.9100%4A1D_1
18.351.075%11.9100%4A18_1
18.351.075%11.9100%4A1B_1
18.318.356%11.9100%3J0L_8
18.318.356%11.9100%3J0O_8
18.379.881%11.9100%3O58_1
18.379.881%11.9100%3O5H_1
18.347.188%11.9100%3O2Z_1
18.347.188%11.9100%3O30_1
18.379.881%11.9100%3IZF_A
18.347.188%11.9100%3IZE_A
18.318.356%11.9100%3KO2_I
18.318.356%11.9100%3KO2_H
18.318.356%11.9100%3KO2_D
18.318.356%11.9100%3KO2_C
18.351.075%11.9100%3I56_0
18.379.881%11.9100%3JYX_5
18.347.188%11.9100%3JYV_A
18.332.756%11.9100%1S1I_3
18.332.756%11.9100%2QEX_0
18.332.756%11.9100%3CPW_0
18.351.075%11.9100%3CCV_0
18.351.075%11.9100%3CCU_0
18.351.075%11.9100%3CCS_0
18.351.075%11.9100%3CCR_0
18.351.075%11.9100%3CCQ_0
18.336.775%11.9100%3CCM_0
18.351.075%11.9100%3CCL_0
18.351.075%11.9100%3CCJ_0
18.351.075%11.9100%3CCE_0
18.351.075%11.9100%3CC7_0
18.351.075%11.9100%3CC2_0
18.363.481%11.9100%2ZKR_0
18.332.756%11.9100%2QA4_0
18.318.356%11.9100%2FTC_R
18.332.756%11.9100%1S72_0
18.351.075%11.9100%1YIT_0
18.351.075%11.9100%1YHQ_0
18.351.075%11.9100%1YJW_0
18.332.756%11.9100%1Q86_A
18.332.756%11.9100%1JJ2_0
18.332.756%11.9100%1KC8_A
18.332.756%11.9100%1FFK_0
18.332.756%11.9100%1FG0_A
18.332.756%11.9100%1FFZ_A
16.416.450%47.03100%4LGT_F
16.416.450%47.03100%4LGT_E
16.432.769%47.03100%4BTD_A
16.432.769%47.03100%4L6J_A
16.432.769%47.03100%4KFI_A
16.432.769%47.03100%4K0Q_A
16.432.769%47.03100%4K0M_A
16.473.888%47.03100%3J3V_A
16.473.888%47.03100%3J3W_A
16.432.769%47.03100%3V6X_A
16.432.769%47.03100%3V6W_A
16.416.450%47.03100%2YMI_DD
16.430.756%47.03100%2YMF_A
16.432.769%47.03100%2J01_A
16.416.450%47.03100%4AQX_C
16.416.450%47.03100%4AQU_C
+ +
+
+ + + +
+

Alignments

+ +
+
+ + + +
+

Chain A, E. Coli 70s-fmetval-trnaval Post-translocation Complex (post4, 50s Subunit)

+

+ Sequence ID: pdb|3J5K|A + Length: 2903 + Number of Matches: 4 +

+
+ + +
+

+ Range 1: 961 to 976 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
32.2 bits(16)0.016/16(100%)0/16(0%)Plus/Plus
+ +
Query        1  CGTCCGTCGTGAAGAG  16
+                ||||||||||||||||
+Subject    961  CGTCCGTCGTGAAGAG  976
+
+
+

+ Range 2: 2591 to 2598 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
16.4 bits(8)47.08/8(100%)0/8(0%)Plus/Plus
+ +
Query        5  CGTCGTGA  12
+                ||||||||
+Subject   2591  CGTCGTGA  2598
+
+
+

+ Range 3: 839 to 845 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query        7  TCGTGAA  13
+                |||||||
+Subject    839  TCGTGAA  845
+
+
+

+ Range 4: 2027 to 2033 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query        9  GTGAAGA  15
+                |||||||
+Subject   2027  GTGAAGA  2033
+
+ +
+ +
+ + + +
+

Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Intermediate Post- Translocation State (post3b, 50s Subunit)

+

+ Sequence ID: pdb|3J5I|A + Length: 2903 + Number of Matches: 4 +

+
+ + +
+

+ Range 1: 961 to 976 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
32.2 bits(16)0.016/16(100%)0/16(0%)Plus/Plus
+ +
Query        1  CGTCCGTCGTGAAGAG  16
+                ||||||||||||||||
+Subject    961  CGTCCGTCGTGAAGAG  976
+
+
+

+ Range 2: 2591 to 2598 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
16.4 bits(8)47.08/8(100%)0/8(0%)Plus/Plus
+ +
Query        5  CGTCGTGA  12
+                ||||||||
+Subject   2591  CGTCGTGA  2598
+
+
+

+ Range 3: 839 to 845 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query        7  TCGTGAA  13
+                |||||||
+Subject    839  TCGTGAA  845
+
+
+

+ Range 4: 2027 to 2033 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query        9  GTGAAGA  15
+                |||||||
+Subject   2027  GTGAAGA  2033
+
+ +
+ +
+ + + +
+

Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Intermediate Post- Translocation State (post3a, 50s Subunit)

+

+ Sequence ID: pdb|3J5G|A + Length: 2903 + Number of Matches: 4 +

+
+ + +
+

+ Range 1: 961 to 976 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
32.2 bits(16)0.016/16(100%)0/16(0%)Plus/Plus
+ +
Query        1  CGTCCGTCGTGAAGAG  16
+                ||||||||||||||||
+Subject    961  CGTCCGTCGTGAAGAG  976
+
+
+

+ Range 2: 2591 to 2598 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
16.4 bits(8)47.08/8(100%)0/8(0%)Plus/Plus
+ +
Query        5  CGTCGTGA  12
+                ||||||||
+Subject   2591  CGTCGTGA  2598
+
+
+

+ Range 3: 839 to 845 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query        7  TCGTGAA  13
+                |||||||
+Subject    839  TCGTGAA  845
+
+
+

+ Range 4: 2027 to 2033 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query        9  GTGAAGA  15
+                |||||||
+Subject   2027  GTGAAGA  2033
+
+ +
+ +
+ + + +
+

Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Intermediate Post- Translocation State (post2b, 50s Subunit)

+

+ Sequence ID: pdb|3J5E|A + Length: 2903 + Number of Matches: 4 +

+
+ + +
+

+ Range 1: 961 to 976 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
32.2 bits(16)0.016/16(100%)0/16(0%)Plus/Plus
+ +
Query        1  CGTCCGTCGTGAAGAG  16
+                ||||||||||||||||
+Subject    961  CGTCCGTCGTGAAGAG  976
+
+
+

+ Range 2: 2591 to 2598 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
16.4 bits(8)47.08/8(100%)0/8(0%)Plus/Plus
+ +
Query        5  CGTCGTGA  12
+                ||||||||
+Subject   2591  CGTCGTGA  2598
+
+
+

+ Range 3: 839 to 845 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query        7  TCGTGAA  13
+                |||||||
+Subject    839  TCGTGAA  845
+
+
+

+ Range 4: 2027 to 2033 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query        9  GTGAAGA  15
+                |||||||
+Subject   2027  GTGAAGA  2033
+
+ +
+ +
+ + + +
+

Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Intermediate Post- Translocation State (post2a, 50s Subunit)

+

+ Sequence ID: pdb|3J5C|A + Length: 2903 + Number of Matches: 4 +

+
+ + +
+

+ Range 1: 961 to 976 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
32.2 bits(16)0.016/16(100%)0/16(0%)Plus/Plus
+ +
Query        1  CGTCCGTCGTGAAGAG  16
+                ||||||||||||||||
+Subject    961  CGTCCGTCGTGAAGAG  976
+
+
+

+ Range 2: 2591 to 2598 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
16.4 bits(8)47.08/8(100%)0/8(0%)Plus/Plus
+ +
Query        5  CGTCGTGA  12
+                ||||||||
+Subject   2591  CGTCGTGA  2598
+
+
+

+ Range 3: 839 to 845 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query        7  TCGTGAA  13
+                |||||||
+Subject    839  TCGTGAA  845
+
+
+

+ Range 4: 2027 to 2033 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query        9  GTGAAGA  15
+                |||||||
+Subject   2027  GTGAAGA  2033
+
+ +
+ +
+ + + +
+

Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Classic Post- Translocation State (post1, 50s Subunit)

+

+ Sequence ID: pdb|3J5A|A + Length: 2903 + Number of Matches: 4 +

+
+ + +
+

+ Range 1: 961 to 976 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
32.2 bits(16)0.016/16(100%)0/16(0%)Plus/Plus
+ +
Query        1  CGTCCGTCGTGAAGAG  16
+                ||||||||||||||||
+Subject    961  CGTCCGTCGTGAAGAG  976
+
+
+

+ Range 2: 2591 to 2598 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
16.4 bits(8)47.08/8(100%)0/8(0%)Plus/Plus
+ +
Query        5  CGTCGTGA  12
+                ||||||||
+Subject   2591  CGTCGTGA  2598
+
+
+

+ Range 3: 839 to 845 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query        7  TCGTGAA  13
+                |||||||
+Subject    839  TCGTGAA  845
+
+
+

+ Range 4: 2027 to 2033 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query        9  GTGAAGA  15
+                |||||||
+Subject   2027  GTGAAGA  2033
+
+ +
+ +
+ + + +
+

Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Hybrid Pre- Translocation State (pre5b, 50s Subunit)

+

+ Sequence ID: pdb|3J58|A + Length: 2903 + Number of Matches: 4 +

+
+ + +
+

+ Range 1: 961 to 976 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
32.2 bits(16)0.016/16(100%)0/16(0%)Plus/Plus
+ +
Query        1  CGTCCGTCGTGAAGAG  16
+                ||||||||||||||||
+Subject    961  CGTCCGTCGTGAAGAG  976
+
+
+

+ Range 2: 2591 to 2598 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
16.4 bits(8)47.08/8(100%)0/8(0%)Plus/Plus
+ +
Query        5  CGTCGTGA  12
+                ||||||||
+Subject   2591  CGTCGTGA  2598
+
+
+

+ Range 3: 839 to 845 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query        7  TCGTGAA  13
+                |||||||
+Subject    839  TCGTGAA  845
+
+
+

+ Range 4: 2027 to 2033 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query        9  GTGAAGA  15
+                |||||||
+Subject   2027  GTGAAGA  2033
+
+ +
+ +
+ + + +
+

Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Hybrid Pre- Translocation State (pre5a, 50s Subunit)

+

+ Sequence ID: pdb|3J56|A + Length: 2903 + Number of Matches: 4 +

+
+ + +
+

+ Range 1: 961 to 976 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
32.2 bits(16)0.016/16(100%)0/16(0%)Plus/Plus
+ +
Query        1  CGTCCGTCGTGAAGAG  16
+                ||||||||||||||||
+Subject    961  CGTCCGTCGTGAAGAG  976
+
+
+

+ Range 2: 2591 to 2598 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
16.4 bits(8)47.08/8(100%)0/8(0%)Plus/Plus
+ +
Query        5  CGTCGTGA  12
+                ||||||||
+Subject   2591  CGTCGTGA  2598
+
+
+

+ Range 3: 839 to 845 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query        7  TCGTGAA  13
+                |||||||
+Subject    839  TCGTGAA  845
+
+
+

+ Range 4: 2027 to 2033 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query        9  GTGAAGA  15
+                |||||||
+Subject   2027  GTGAAGA  2033
+
+ +
+ +
+ + + +
+

Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Hybrid Pre- Translocation State (pre4, 50s Subunit)

+

+ Sequence ID: pdb|3J54|A + Length: 2903 + Number of Matches: 4 +

+
+ + +
+

+ Range 1: 961 to 976 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
32.2 bits(16)0.016/16(100%)0/16(0%)Plus/Plus
+ +
Query        1  CGTCCGTCGTGAAGAG  16
+                ||||||||||||||||
+Subject    961  CGTCCGTCGTGAAGAG  976
+
+
+

+ Range 2: 2591 to 2598 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
16.4 bits(8)47.08/8(100%)0/8(0%)Plus/Plus
+ +
Query        5  CGTCGTGA  12
+                ||||||||
+Subject   2591  CGTCGTGA  2598
+
+
+

+ Range 3: 839 to 845 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query        7  TCGTGAA  13
+                |||||||
+Subject    839  TCGTGAA  845
+
+
+

+ Range 4: 2027 to 2033 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query        9  GTGAAGA  15
+                |||||||
+Subject   2027  GTGAAGA  2033
+
+ +
+ +
+ + + +
+

Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Classic Pre- Translocation State (pre1a, 50s Subunit)

+

+ Sequence ID: pdb|3J52|A + Length: 2903 + Number of Matches: 4 +

+
+ + +
+

+ Range 1: 961 to 976 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
32.2 bits(16)0.016/16(100%)0/16(0%)Plus/Plus
+ +
Query        1  CGTCCGTCGTGAAGAG  16
+                ||||||||||||||||
+Subject    961  CGTCCGTCGTGAAGAG  976
+
+
+

+ Range 2: 2591 to 2598 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
16.4 bits(8)47.08/8(100%)0/8(0%)Plus/Plus
+ +
Query        5  CGTCGTGA  12
+                ||||||||
+Subject   2591  CGTCGTGA  2598
+
+
+

+ Range 3: 839 to 845 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query        7  TCGTGAA  13
+                |||||||
+Subject    839  TCGTGAA  845
+
+
+

+ Range 4: 2027 to 2033 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query        9  GTGAAGA  15
+                |||||||
+Subject   2027  GTGAAGA  2033
+
+ +
+ +
+ + + +
+

Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Intermediate Pre- Translocation State (pre3, 50s Subunit)

+

+ Sequence ID: pdb|3J51|A + Length: 2903 + Number of Matches: 4 +

+
+ + +
+

+ Range 1: 961 to 976 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
32.2 bits(16)0.016/16(100%)0/16(0%)Plus/Plus
+ +
Query        1  CGTCCGTCGTGAAGAG  16
+                ||||||||||||||||
+Subject    961  CGTCCGTCGTGAAGAG  976
+
+
+

+ Range 2: 2591 to 2598 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
16.4 bits(8)47.08/8(100%)0/8(0%)Plus/Plus
+ +
Query        5  CGTCGTGA  12
+                ||||||||
+Subject   2591  CGTCGTGA  2598
+
+
+

+ Range 3: 839 to 845 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query        7  TCGTGAA  13
+                |||||||
+Subject    839  TCGTGAA  845
+
+
+

+ Range 4: 2027 to 2033 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query        9  GTGAAGA  15
+                |||||||
+Subject   2027  GTGAAGA  2033
+
+ +
+ +
+ + + +
+

Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Intermediate Pre- Translocation State (pre2, 50s Subunit)

+

+ Sequence ID: pdb|3J50|A + Length: 2903 + Number of Matches: 4 +

+
+ + +
+

+ Range 1: 961 to 976 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
32.2 bits(16)0.016/16(100%)0/16(0%)Plus/Plus
+ +
Query        1  CGTCCGTCGTGAAGAG  16
+                ||||||||||||||||
+Subject    961  CGTCCGTCGTGAAGAG  976
+
+
+

+ Range 2: 2591 to 2598 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
16.4 bits(8)47.08/8(100%)0/8(0%)Plus/Plus
+ +
Query        5  CGTCGTGA  12
+                ||||||||
+Subject   2591  CGTCGTGA  2598
+
+
+

+ Range 3: 839 to 845 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query        7  TCGTGAA  13
+                |||||||
+Subject    839  TCGTGAA  845
+
+
+

+ Range 4: 2027 to 2033 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query        9  GTGAAGA  15
+                |||||||
+Subject   2027  GTGAAGA  2033
+
+ +
+ +
+ + + +
+

Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Classic Pre- Translocation State (pre1b, 50s Subunit)

+

+ Sequence ID: pdb|3J4X|A + Length: 2903 + Number of Matches: 4 +

+
+ + +
+

+ Range 1: 961 to 976 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
32.2 bits(16)0.016/16(100%)0/16(0%)Plus/Plus
+ +
Query        1  CGTCCGTCGTGAAGAG  16
+                ||||||||||||||||
+Subject    961  CGTCCGTCGTGAAGAG  976
+
+
+

+ Range 2: 2591 to 2598 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
16.4 bits(8)47.08/8(100%)0/8(0%)Plus/Plus
+ +
Query        5  CGTCGTGA  12
+                ||||||||
+Subject   2591  CGTCGTGA  2598
+
+
+

+ Range 3: 839 to 845 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query        7  TCGTGAA  13
+                |||||||
+Subject    839  TCGTGAA  845
+
+
+

+ Range 4: 2027 to 2033 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query        9  GTGAAGA  15
+                |||||||
+Subject   2027  GTGAAGA  2033
+
+ +
+ +
+ + + +
+

Chain A, Tetracycline Resistance Protein Tet(o) Bound To The Ribosome

+

+ Sequence ID: pdb|3J37|A + Length: 2904 + Number of Matches: 3 +

+
+ + +
+

+ Range 1: 961 to 976 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
32.2 bits(16)0.016/16(100%)0/16(0%)Plus/Plus
+ +
Query        1  CGTCCGTCGTGAAGAG  16
+                ||||||||||||||||
+Subject    961  CGTCCGTCGTGAAGAG  976
+
+
+

+ Range 2: 2591 to 2598 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
16.4 bits(8)47.08/8(100%)0/8(0%)Plus/Plus
+ +
Query        5  CGTCGTGA  12
+                ||||||||
+Subject   2591  CGTCGTGA  2598
+
+
+

+ Range 3: 839 to 845 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query        7  TCGTGAA  13
+                |||||||
+Subject    839  TCGTGAA  845
+
+ +
+ +
+ + + +
+

Chain B, Structural Insights Into Cognate Vs. Near-Cognate Discrimination During Decoding. This Entry Contains The Large Subunit Of A Ribosome Programmed With A Near-Cognate Codon.

+

+ Sequence ID: pdb|3IZT|B + Length: 2904 + Number of Matches: 3 +

+
+ + + See 7 more title(s) + + + + +
+

+ Range 1: 961 to 976 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
32.2 bits(16)0.016/16(100%)0/16(0%)Plus/Plus
+ +
Query        1  CGTCCGTCGTGAAGAG  16
+                ||||||||||||||||
+Subject    961  CGTCCGTCGTGAAGAG  976
+
+
+

+ Range 2: 2591 to 2598 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
16.4 bits(8)47.08/8(100%)0/8(0%)Plus/Plus
+ +
Query        5  CGTCGTGA  12
+                ||||||||
+Subject   2591  CGTCGTGA  2598
+
+
+

+ Range 3: 839 to 845 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query        7  TCGTGAA  13
+                |||||||
+Subject    839  TCGTGAA  845
+
+ +
+ +
+ + + +
+

Chain B, Ternary Complex-Bound E.Coli 70s Ribosome. This Entry Consists Of The 50s Subunit.

+

+ Sequence ID: pdb|3FIK|B + Length: 2903 + Number of Matches: 4 +

+
+ + + See 19 more title(s) + + + + +
+

+ Range 1: 961 to 976 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
32.2 bits(16)0.016/16(100%)0/16(0%)Plus/Plus
+ +
Query        1  CGTCCGTCGTGAAGAG  16
+                ||||||||||||||||
+Subject    961  CGTCCGTCGTGAAGAG  976
+
+
+

+ Range 2: 2591 to 2598 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
16.4 bits(8)47.08/8(100%)0/8(0%)Plus/Plus
+ +
Query        5  CGTCGTGA  12
+                ||||||||
+Subject   2591  CGTCGTGA  2598
+
+
+

+ Range 3: 839 to 845 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query        7  TCGTGAA  13
+                |||||||
+Subject    839  TCGTGAA  845
+
+
+

+ Range 4: 2027 to 2033 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query        9  GTGAAGA  15
+                |||||||
+Subject   2027  GTGAAGA  2033
+
+ +
+ +
+ + + +
+

Chain B, Structure Of The 50s Subunit Of E. Coli Ribosome In Pre-Accommodation State

+

+ Sequence ID: pdb|3E1B|B + Length: 2903 + Number of Matches: 4 +

+
+ + + See 1 more title(s) + + + + +
+

+ Range 1: 961 to 976 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
32.2 bits(16)0.016/16(100%)0/16(0%)Plus/Plus
+ +
Query        1  CGTCCGTCGTGAAGAG  16
+                ||||||||||||||||
+Subject    961  CGTCCGTCGTGAAGAG  976
+
+
+

+ Range 2: 2591 to 2598 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
16.4 bits(8)47.08/8(100%)0/8(0%)Plus/Plus
+ +
Query        5  CGTCGTGA  12
+                ||||||||
+Subject   2591  CGTCGTGA  2598
+
+
+

+ Range 3: 839 to 845 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query        7  TCGTGAA  13
+                |||||||
+Subject    839  TCGTGAA  845
+
+
+

+ Range 4: 2027 to 2033 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query        9  GTGAAGA  15
+                |||||||
+Subject   2027  GTGAAGA  2033
+
+ +
+ +
+ + + +
+

Chain 0, Structure Of The 50s Subunit Of A Secm-Stalled E. Coli Ribosome Complex Obtained By Fitting Atomic Models For Rna And Protein Components Into Cryo-Em Map Emd-1143

+

+ Sequence ID: pdb|2GYC|0 + Length: 2740 + Number of Matches: 4 +

+
+ + +
+

+ Range 1: 889 to 904 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
32.2 bits(16)0.016/16(100%)0/16(0%)Plus/Plus
+ +
Query        1  CGTCCGTCGTGAAGAG  16
+                ||||||||||||||||
+Subject    889  CGTCCGTCGTGAAGAG  904
+
+
+

+ Range 2: 2453 to 2460 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
16.4 bits(8)47.08/8(100%)0/8(0%)Plus/Plus
+ +
Query        5  CGTCGTGA  12
+                ||||||||
+Subject   2453  CGTCGTGA  2460
+
+
+

+ Range 3: 776 to 782 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query        7  TCGTGAA  13
+                |||||||
+Subject    776  TCGTGAA  782
+
+
+

+ Range 4: 1910 to 1916 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query        9  GTGAAGA  15
+                |||||||
+Subject   1910  GTGAAGA  1916
+
+ +
+ +
+ + + +
+

Chain 0, Structure Of The 50s Subunit Of A Pre-Translocational E. Coli Ribosome Obtained By Fitting Atomic Models For Rna And Protein Components Into Cryo-Em Map Emd-1056

+

+ Sequence ID: pdb|2GYA|0 + Length: 2740 + Number of Matches: 4 +

+
+ + +
+

+ Range 1: 889 to 904 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
32.2 bits(16)0.016/16(100%)0/16(0%)Plus/Plus
+ +
Query        1  CGTCCGTCGTGAAGAG  16
+                ||||||||||||||||
+Subject    889  CGTCCGTCGTGAAGAG  904
+
+
+

+ Range 2: 2453 to 2460 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
16.4 bits(8)47.08/8(100%)0/8(0%)Plus/Plus
+ +
Query        5  CGTCGTGA  12
+                ||||||||
+Subject   2453  CGTCGTGA  2460
+
+
+

+ Range 3: 776 to 782 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query        7  TCGTGAA  13
+                |||||||
+Subject    776  TCGTGAA  782
+
+
+

+ Range 4: 1910 to 1916 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query        9  GTGAAGA  15
+                |||||||
+Subject   1910  GTGAAGA  1916
+
+ +
+ +
+ + + +
+

Chain B, Crystal Structure Of Ribosome With Messenger Rna And The Anticodon Stem-Loop Of P-Site Trna. This File Contains The 50s Subunit Of One 70s Ribosome. The Entire Crystal Structure Contains Two 70s Ribosomes And Is Described In Remark 400.

+

+ Sequence ID: pdb|2I2V|B + Length: 2904 + Number of Matches: 4 +

+
+ + +
+

+ Range 1: 961 to 976 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
32.2 bits(16)0.016/16(100%)0/16(0%)Plus/Plus
+ +
Query        1  CGTCCGTCGTGAAGAG  16
+                ||||||||||||||||
+Subject    961  CGTCCGTCGTGAAGAG  976
+
+
+

+ Range 2: 2591 to 2598 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
16.4 bits(8)47.08/8(100%)0/8(0%)Plus/Plus
+ +
Query        5  CGTCGTGA  12
+                ||||||||
+Subject   2591  CGTCGTGA  2598
+
+
+

+ Range 3: 839 to 845 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query        7  TCGTGAA  13
+                |||||||
+Subject    839  TCGTGAA  845
+
+
+

+ Range 4: 2027 to 2033 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query        9  GTGAAGA  15
+                |||||||
+Subject   2027  GTGAAGA  2033
+
+ +
+ +
+ + + +
+

Chain B, Crystal Structure Of The Bacterial Ribosome From Escherichia Coli At 3.5 A Resolution. This File Contains The 50s Subunit Of One 70s Ribosome. The Entire Crystal Structure Contains Two 70s Ribosomes And Is Described In Remark 400.

+

+ Sequence ID: pdb|2AW4|B + Length: 2904 + Number of Matches: 4 +

+
+ + + See 38 more title(s) + + + + +
+

+ Range 1: 961 to 976 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
32.2 bits(16)0.016/16(100%)0/16(0%)Plus/Plus
+ +
Query        1  CGTCCGTCGTGAAGAG  16
+                ||||||||||||||||
+Subject    961  CGTCCGTCGTGAAGAG  976
+
+
+

+ Range 2: 2591 to 2598 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
16.4 bits(8)47.08/8(100%)0/8(0%)Plus/Plus
+ +
Query        5  CGTCGTGA  12
+                ||||||||
+Subject   2591  CGTCGTGA  2598
+
+
+

+ Range 3: 839 to 845 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query        7  TCGTGAA  13
+                |||||||
+Subject    839  TCGTGAA  845
+
+
+

+ Range 4: 2027 to 2033 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query        9  GTGAAGA  15
+                |||||||
+Subject   2027  GTGAAGA  2033
+
+ +
+ +
+ + + +
+

Chain B, Crystal Structure Of The Bacterial Ribosome From Escherichia Coli At 3.5 A Resolution. This File Contains The 50s Subunit Of The Second 70s Ribosome. The Entire Crystal Structure Contains Two 70s Ribosomes And Is Described In Remark 400.

+

+ Sequence ID: pdb|2AWB|B + Length: 2904 + Number of Matches: 4 +

+
+ + + See 2 more title(s) + + + + +
+

+ Range 1: 961 to 976 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
32.2 bits(16)0.016/16(100%)0/16(0%)Plus/Plus
+ +
Query        1  CGTCCGTCGTGAAGAG  16
+                ||||||||||||||||
+Subject    961  CGTCCGTCGTGAAGAG  976
+
+
+

+ Range 2: 2591 to 2598 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
16.4 bits(8)47.08/8(100%)0/8(0%)Plus/Plus
+ +
Query        5  CGTCGTGA  12
+                ||||||||
+Subject   2591  CGTCGTGA  2598
+
+
+

+ Range 3: 839 to 845 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query        7  TCGTGAA  13
+                |||||||
+Subject    839  TCGTGAA  845
+
+
+

+ Range 4: 2027 to 2033 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query        9  GTGAAGA  15
+                |||||||
+Subject   2027  GTGAAGA  2033
+
+ +
+ +
+ + + +
+

Chain B, Crystal Structure Of The Bacterial Ribosome From Escherichia Coli In Complex With The Antibiotic Kasugamyin At 3.5a Resolution. This File Contains The 50s Subunit Of One 70s Ribosome. The Entire Crystal Structure Contains Two 70s Ribosomes And Is Described In Remark 400.

+

+ Sequence ID: pdb|1VS6|B + Length: 2904 + Number of Matches: 4 +

+
+ + + See 6 more title(s) + + + + +
+

+ Range 1: 961 to 976 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
32.2 bits(16)0.016/16(100%)0/16(0%)Plus/Plus
+ +
Query        1  CGTCCGTCGTGAAGAG  16
+                ||||||||||||||||
+Subject    961  CGTCCGTCGTGAAGAG  976
+
+
+

+ Range 2: 2591 to 2598 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
16.4 bits(8)47.08/8(100%)0/8(0%)Plus/Plus
+ +
Query        5  CGTCGTGA  12
+                ||||||||
+Subject   2591  CGTCGTGA  2598
+
+
+

+ Range 3: 839 to 845 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query        7  TCGTGAA  13
+                |||||||
+Subject    839  TCGTGAA  845
+
+
+

+ Range 4: 2027 to 2033 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query        9  GTGAAGA  15
+                |||||||
+Subject   2027  GTGAAGA  2033
+
+ +
+ +
+ + + +
+

Chain 0, Real Space Refined Coordinates Of The 50s Subunit Fitted Into The Low Resolution Cryo-Em Map Of The Ef-G.Gtp State Of E. Coli 70s Ribosome

+

+ Sequence ID: pdb|1P85|0 + Length: 2904 + Number of Matches: 4 +

+
+ + + See 1 more title(s) + + + + +
+

+ Range 1: 961 to 976 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
32.2 bits(16)0.016/16(100%)0/16(0%)Plus/Plus
+ +
Query        1  CGTCCGTCGTGAAGAG  16
+                ||||||||||||||||
+Subject    961  CGTCCGTCGTGAAGAG  976
+
+
+

+ Range 2: 2591 to 2598 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
16.4 bits(8)47.08/8(100%)0/8(0%)Plus/Plus
+ +
Query        5  CGTCGTGA  12
+                ||||||||
+Subject   2591  CGTCGTGA  2598
+
+
+

+ Range 3: 839 to 845 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query        7  TCGTGAA  13
+                |||||||
+Subject    839  TCGTGAA  845
+
+
+

+ Range 4: 2027 to 2033 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query        9  GTGAAGA  15
+                |||||||
+Subject   2027  GTGAAGA  2033
+
+ +
+ +
+ + + +
+

Chain B, 23s Rrna Structure Fitted To A Cryo-Electron Microscopic Map At 7.5 Angstroms Resolution

+

+ Sequence ID: pdb|1C2W|B + Length: 2904 + Number of Matches: 2 +

+
+ + +
+

+ Range 1: 961 to 973 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
26.3 bits(13)0.013/13(100%)0/13(0%)Plus/Plus
+ +
Query        1  CGTCCGTCGTGAA  13
+                |||||||||||||
+Subject    961  CGTCCGTCGTGAA  973
+
+
+

+ Range 2: 839 to 845 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query        7  TCGTGAA  13
+                |||||||
+Subject    839  TCGTGAA  845
+
+ +
+ +
+ + + +
+

Chain 1, Structure Of The Methanococcus Jannaschii Ribosome-secyebeta Channel Complex (50s Ribosomal Subunit)

+

+ Sequence ID: pdb|3J44|1 + Length: 3049 + Number of Matches: 2 +

+
+ + +
+

+ Range 1: 651 to 663 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
18.3 bits(9)11.912/13(92%)0/13(0%)Plus/Plus
+ +
Query        1  CGTCCGTCGTGAA  13
+                |||||||| ||||
+Subject    651  CGTCCGTCTTGAA  663
+
+
+

+ Range 2: 2705 to 2713 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
18.3 bits(9)11.99/9(100%)0/9(0%)Plus/Plus
+ +
Query        4  CCGTCGTGA  12
+                |||||||||
+Subject   2705  CCGTCGTGA  2713
+
+ +
+ +
+ + + +
+

Chain 1, Promiscuous Behavior Of Proteins In Archaeal Ribosomes Revealed By Cryo-em: Implications For Evolution Of Eukaryotic Ribosomes (50s Ribosomal Rna)

+

+ Sequence ID: pdb|3J2L|1 + Length: 3049 + Number of Matches: 2 +

+
+ + +
+

+ Range 1: 651 to 663 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
18.3 bits(9)11.912/13(92%)0/13(0%)Plus/Plus
+ +
Query        1  CGTCCGTCGTGAA  13
+                |||||||| ||||
+Subject    651  CGTCCGTCTTGAA  663
+
+
+

+ Range 2: 2705 to 2713 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
18.3 bits(9)11.99/9(100%)0/9(0%)Plus/Plus
+ +
Query        4  CCGTCGTGA  12
+                |||||||||
+Subject   2705  CCGTCGTGA  2713
+
+ +
+ +
+ + + +
+

Chain a, Model Of The Large Subunit Rna Based On A 5.5 A Cryo-em Map Of Triticum Aestivum Translating 80s Ribosome

+

+ Sequence ID: pdb|3J62|AA + Length: 3391 + Number of Matches: 5 +

+
+ + +
+

+ Range 1: 2961 to 2969 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
18.3 bits(9)11.99/9(100%)0/9(0%)Plus/Plus
+ +
Query        4  CCGTCGTGA  12
+                |||||||||
+Subject   2961  CCGTCGTGA  2969
+
+
+

+ Range 2: 177 to 170 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
16.4 bits(8)47.08/8(100%)0/8(0%)Plus/Minus
+ +
Query        2  GTCCGTCG  9
+                ||||||||
+Subject    177  GTCCGTCG  170
+
+
+

+ Range 3: 553 to 559 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query        4  CCGTCGT  10
+                |||||||
+Subject    553  CCGTCGT  559
+
+
+

+ Range 4: 2048 to 2042 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Minus
+ +
Query        2  GTCCGTC  8
+                |||||||
+Subject   2048  GTCCGTC  2042
+
+
+

+ Range 5: 2211 to 2217 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query        9  GTGAAGA  15
+                |||||||
+Subject   2211  GTGAAGA  2217
+
+ +
+ +
+ + + +
+

Chain A, 39s Large Subunit Of The Porcine Mitochondrial Ribosome

+

+ Sequence ID: pdb|4CE4|A + Length: 1570 + Number of Matches: 1 +

+
+ + +
+

+ Range 1: 1020 to 1028 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
18.3 bits(9)11.99/9(100%)0/9(0%)Plus/Plus
+ +
Query        8  CGTGAAGAG  16
+                |||||||||
+Subject   1020  CGTGAAGAG  1028
+
+ +
+ +
+ + + +
+

Chain 5, Cryo-em Reconstruction Of The 80s-eif5b-met-itrnamet Eukaryotic Translation Initiation Complex

+

+ Sequence ID: pdb|4BYP|5 + Length: 3396 + Number of Matches: 5 +

+
+ + +
+

+ Range 1: 2959 to 2967 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
18.3 bits(9)11.99/9(100%)0/9(0%)Plus/Plus
+ +
Query        4  CCGTCGTGA  12
+                |||||||||
+Subject   2959  CCGTCGTGA  2967
+
+
+

+ Range 2: 1634 to 1627 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
16.4 bits(8)47.08/8(100%)0/8(0%)Plus/Minus
+ +
Query        8  CGTGAAGA  15
+                ||||||||
+Subject   1634  CGTGAAGA  1627
+
+
+

+ Range 3: 2435 to 2442 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
16.4 bits(8)47.08/8(100%)0/8(0%)Plus/Plus
+ +
Query        9  GTGAAGAG  16
+                ||||||||
+Subject   2435  GTGAAGAG  2442
+
+
+

+ Range 4: 1100 to 1106 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query       10  TGAAGAG  16
+                |||||||
+Subject   1100  TGAAGAG  1106
+
+
+

+ Range 5: 2216 to 2222 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query        9  GTGAAGA  15
+                |||||||
+Subject   2216  GTGAAGA  2222
+
+ +
+ +
+ + + +
+

Chain 5, Cryo-em Reconstruction Of The 80s-eif5b-met-itrnamet Eukaryotic Translation Initiation Complex

+

+ Sequence ID: pdb|4BYW|5 + Length: 3396 + Number of Matches: 5 +

+
+ + +
+

+ Range 1: 2959 to 2967 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
18.3 bits(9)11.99/9(100%)0/9(0%)Plus/Plus
+ +
Query        4  CCGTCGTGA  12
+                |||||||||
+Subject   2959  CCGTCGTGA  2967
+
+
+

+ Range 2: 1634 to 1627 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
16.4 bits(8)47.08/8(100%)0/8(0%)Plus/Minus
+ +
Query        8  CGTGAAGA  15
+                ||||||||
+Subject   1634  CGTGAAGA  1627
+
+
+

+ Range 3: 2435 to 2442 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
16.4 bits(8)47.08/8(100%)0/8(0%)Plus/Plus
+ +
Query        9  GTGAAGAG  16
+                ||||||||
+Subject   2435  GTGAAGAG  2442
+
+
+

+ Range 4: 1100 to 1106 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query       10  TGAAGAG  16
+                |||||||
+Subject   1100  TGAAGAG  1106
+
+
+

+ Range 5: 2216 to 2222 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query        9  GTGAAGA  15
+                |||||||
+Subject   2216  GTGAAGA  2222
+
+ +
+ +
+ + + +
+

Chain 0, The Re-refined Crystal Structure Of The Haloarcula Marismortui Large Ribosomal Subunit At 2.4 Angstrom Resolution: More Complete Structure Of The L7/l12 And L1 Stalk, L5 And Lx Proteins

+

+ Sequence ID: pdb|4HUB|0 + Length: 2910 + Number of Matches: 3 +

+
+ + +
+

+ Range 1: 298 to 290 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
18.3 bits(9)11.99/9(100%)0/9(0%)Plus/Minus
+ +
Query        7  TCGTGAAGA  15
+                |||||||||
+Subject    298  TCGTGAAGA  290
+
+
+

+ Range 2: 2618 to 2626 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
18.3 bits(9)11.99/9(100%)0/9(0%)Plus/Plus
+ +
Query        4  CCGTCGTGA  12
+                |||||||||
+Subject   2618  CCGTCGTGA  2626
+
+
+

+ Range 3: 2599 to 2605 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query        6  GTCGTGA  12
+                |||||||
+Subject   2599  GTCGTGA  2605
+
+ +
+ +
+ + + +
+

Chain 5, Structure Of The H. Sapiens 60s Rrna

+

+ Sequence ID: pdb|3J3F|5 + Length: 5070 + Number of Matches: 8 +

+
+ + +
+

+ Range 1: 4536 to 4544 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
18.3 bits(9)11.99/9(100%)0/9(0%)Plus/Plus
+ +
Query        4  CCGTCGTGA  12
+                |||||||||
+Subject   4536  CCGTCGTGA  4544
+
+
+

+ Range 2: 765 to 772 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
16.4 bits(8)47.08/8(100%)0/8(0%)Plus/Plus
+ +
Query        1  CGTCCGTC  8
+                ||||||||
+Subject    765  CGTCCGTC  772
+
+
+

+ Range 3: 769 to 776 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
16.4 bits(8)47.08/8(100%)0/8(0%)Plus/Plus
+ +
Query        1  CGTCCGTC  8
+                ||||||||
+Subject    769  CGTCCGTC  776
+
+
+

+ Range 4: 773 to 780 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
16.4 bits(8)47.08/8(100%)0/8(0%)Plus/Plus
+ +
Query        1  CGTCCGTC  8
+                ||||||||
+Subject    773  CGTCCGTC  780
+
+
+

+ Range 5: 777 to 784 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
16.4 bits(8)47.08/8(100%)0/8(0%)Plus/Plus
+ +
Query        1  CGTCCGTC  8
+                ||||||||
+Subject    777  CGTCCGTC  784
+
+
+

+ Range 6: 3939 to 3946 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
16.4 bits(8)47.08/8(100%)0/8(0%)Plus/Plus
+ +
Query        9  GTGAAGAG  16
+                ||||||||
+Subject   3939  GTGAAGAG  3946
+
+
+

+ Range 7: 393 to 399 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query       10  TGAAGAG  16
+                |||||||
+Subject    393  TGAAGAG  399
+
+
+

+ Range 8: 3720 to 3726 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query        9  GTGAAGA  15
+                |||||||
+Subject   3720  GTGAAGA  3726
+
+ +
+ +
+ + + +
+

Chain 5, Structure Of The D. Melanogaster 60s Rrna

+

+ Sequence ID: pdb|3J3E|5 + Length: 3970 + Number of Matches: 4 +

+
+ + +
+

+ Range 1: 3490 to 3498 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
18.3 bits(9)11.99/9(100%)0/9(0%)Plus/Plus
+ +
Query        4  CCGTCGTGA  12
+                |||||||||
+Subject   3490  CCGTCGTGA  3498
+
+
+

+ Range 2: 2177 to 2184 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
16.4 bits(8)47.08/8(100%)0/8(0%)Plus/Plus
+ +
Query        9  GTGAAGAG  16
+                ||||||||
+Subject   2177  GTGAAGAG  2184
+
+
+

+ Range 3: 2594 to 2600 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query        9  GTGAAGA  15
+                |||||||
+Subject   2594  GTGAAGA  2600
+
+
+

+ Range 4: 3627 to 3633 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query        1  CGTCCGT  7
+                |||||||
+Subject   3627  CGTCCGT  3633
+
+ +
+ +
+ + + +
+

Chain B, High_resolution Cryo-electron Microscopy Structure Of The Trypanosoma Brucei Ribosome

+

+ Sequence ID: pdb|3ZEX|B + Length: 1465 + Number of Matches: 2 +

+
+ + +
+

+ Range 1: 1334 to 1342 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
18.3 bits(9)11.99/9(100%)0/9(0%)Plus/Plus
+ +
Query        4  CCGTCGTGA  12
+                |||||||||
+Subject   1334  CCGTCGTGA  1342
+
+
+

+ Range 2: 705 to 711 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query       10  TGAAGAG  16
+                |||||||
+Subject    705  TGAAGAG  711
+
+ +
+ +
+ + + +
+

Chain 0, Crystal Structure Of Enhanced Macrolide Bound To 50s Ribosomal Subunit

+

+ Sequence ID: pdb|3OW2|0 + Length: 2902 + Number of Matches: 2 +

+
+ + +
+

+ Range 1: 2613 to 2621 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
18.3 bits(9)11.99/9(100%)0/9(0%)Plus/Plus
+ +
Query        4  CCGTCGTGA  12
+                |||||||||
+Subject   2613  CCGTCGTGA  2621
+
+
+

+ Range 2: 2594 to 2600 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query        6  GTCGTGA  12
+                |||||||
+Subject   2594  GTCGTGA  2600
+
+ +
+ +
+ + + +
+

Chain 0, The Cryo-em Structure Of The Archaeal 50s Ribosomal Subunit In Complex With Initiation Factor 6

+

+ Sequence ID: pdb|4ADX|0 + Length: 2923 + Number of Matches: 3 +

+
+ + +
+

+ Range 1: 305 to 297 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
18.3 bits(9)11.99/9(100%)0/9(0%)Plus/Minus
+ +
Query        7  TCGTGAAGA  15
+                |||||||||
+Subject    305  TCGTGAAGA  297
+
+
+

+ Range 2: 2625 to 2633 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
18.3 bits(9)11.99/9(100%)0/9(0%)Plus/Plus
+ +
Query        4  CCGTCGTGA  12
+                |||||||||
+Subject   2625  CCGTCGTGA  2633
+
+
+

+ Range 3: 2606 to 2612 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query        6  GTCGTGA  12
+                |||||||
+Subject   2606  GTCGTGA  2612
+
+ +
+ +
+ + + +
+

Chain 6, The Structure Of The Eukaryotic Ribosome At 3.0 A Resolution. This Entry Contains Ribosomal Rna And Ions Of The 40s Subunit, Ribosome B

+

+ Sequence ID: pdb|3U5F|6 + Length: 1800 + Number of Matches: 3 +

+
+ + +
+

+ Range 1: 1528 to 1536 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
18.3 bits(9)11.99/9(100%)0/9(0%)Plus/Plus
+ +
Query        3  TCCGTCGTG  11
+                |||||||||
+Subject   1528  TCCGTCGTG  1536
+
+
+

+ Range 2: 1006 to 1012 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query        4  CCGTCGT  10
+                |||||||
+Subject   1006  CCGTCGT  1012
+
+
+

+ Range 3: 1569 to 1563 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Minus
+ +
Query       10  TGAAGAG  16
+                |||||||
+Subject   1569  TGAAGAG  1563
+
+ +
+ +
+ + + +
+

Chain 2, The Structure Of The Eukaryotic Ribosome At 3.0 A Resolution. This Entry Contains Ribosomal Rna And Ions Of The 40s Subunit, Ribosome A

+

+ Sequence ID: pdb|3U5B|2 + Length: 1800 + Number of Matches: 3 +

+
+ + + See 2 more title(s) + + + + +
+

+ Range 1: 1528 to 1536 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
18.3 bits(9)11.99/9(100%)0/9(0%)Plus/Plus
+ +
Query        3  TCCGTCGTG  11
+                |||||||||
+Subject   1528  TCCGTCGTG  1536
+
+
+

+ Range 2: 1006 to 1012 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query        4  CCGTCGT  10
+                |||||||
+Subject   1006  CCGTCGT  1012
+
+
+

+ Range 3: 1569 to 1563 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Minus
+ +
Query       10  TGAAGAG  16
+                |||||||
+Subject   1569  TGAAGAG  1563
+
+ +
+ +
+ + + +
+

Chain 1, T.Thermophila 60s Ribosomal Subunit In Complex With Initiation Factor 6. This File Contains 26s Rrna And Proteins Of Molecule 4.

+

+ Sequence ID: pdb|4A1D|1 + Length: 3119 + Number of Matches: 3 +

+
+ + +
+

+ Range 1: 2280 to 2288 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
18.3 bits(9)11.99/9(100%)0/9(0%)Plus/Plus
+ +
Query        7  TCGTGAAGA  15
+                |||||||||
+Subject   2280  TCGTGAAGA  2288
+
+
+

+ Range 2: 2714 to 2722 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
18.3 bits(9)11.99/9(100%)0/9(0%)Plus/Plus
+ +
Query        4  CCGTCGTGA  12
+                |||||||||
+Subject   2714  CCGTCGTGA  2722
+
+
+

+ Range 3: 2838 to 2844 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query        8  CGTGAAG  14
+                |||||||
+Subject   2838  CGTGAAG  2844
+
+ +
+ +
+ + + +
+

Chain 1, T.Thermophila 60s Ribosomal Subunit In Complex With Initiation Factor 6. This File Contains 26s Rrna And Proteins Of Molecule 1

+

+ Sequence ID: pdb|4A18|1 + Length: 3354 + Number of Matches: 3 +

+
+ + +
+

+ Range 1: 2513 to 2521 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
18.3 bits(9)11.99/9(100%)0/9(0%)Plus/Plus
+ +
Query        7  TCGTGAAGA  15
+                |||||||||
+Subject   2513  TCGTGAAGA  2521
+
+
+

+ Range 2: 2947 to 2955 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
18.3 bits(9)11.99/9(100%)0/9(0%)Plus/Plus
+ +
Query        4  CCGTCGTGA  12
+                |||||||||
+Subject   2947  CCGTCGTGA  2955
+
+
+

+ Range 3: 3071 to 3077 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query        8  CGTGAAG  14
+                |||||||
+Subject   3071  CGTGAAG  3077
+
+ +
+ +
+ + + +
+

Chain 1, T.Thermophila 60s Ribosomal Subunit In Complex With Initiation Factor 6. This File Contains 26s Rrna And Proteins Of Molecule 3.

+

+ Sequence ID: pdb|4A1B|1 + Length: 3354 + Number of Matches: 3 +

+
+ + + See 1 more title(s) + + + + +
+

+ Range 1: 2513 to 2521 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
18.3 bits(9)11.99/9(100%)0/9(0%)Plus/Plus
+ +
Query        7  TCGTGAAGA  15
+                |||||||||
+Subject   2513  TCGTGAAGA  2521
+
+
+

+ Range 2: 2947 to 2955 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
18.3 bits(9)11.99/9(100%)0/9(0%)Plus/Plus
+ +
Query        4  CCGTCGTGA  12
+                |||||||||
+Subject   2947  CCGTCGTGA  2955
+
+
+

+ Range 3: 3071 to 3077 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query        8  CGTGAAG  14
+                |||||||
+Subject   3071  CGTGAAG  3077
+
+ +
+ +
+ + + +
+

Chain 8, Core Of Mammalian 80s Pre-Ribosome In Complex With Trnas Fitted To A 9.8a Cryo-Em Map: Classic Pre State 1

+

+ Sequence ID: pdb|3J0L|8 + Length: 20 + Number of Matches: 1 +

+
+ + +
+

+ Range 1: 3 to 11 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
18.3 bits(9)11.99/9(100%)0/9(0%)Plus/Plus
+ +
Query        4  CCGTCGTGA  12
+                |||||||||
+Subject      3  CCGTCGTGA  11
+
+ +
+ +
+ + + +
+

Chain 8, Core Of Mammalian 80s Pre-Ribosome In Complex With Trnas Fitted To A 9a Cryo-Em Map: Classic Pre State 2

+

+ Sequence ID: pdb|3J0O|8 + Length: 20 + Number of Matches: 1 +

+
+ + +
+

+ Range 1: 3 to 11 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
18.3 bits(9)11.99/9(100%)0/9(0%)Plus/Plus
+ +
Query        4  CCGTCGTGA  12
+                |||||||||
+Subject      3  CCGTCGTGA  11
+
+ +
+ +
+ + + +
+

Chain 1, Yeast 80s Ribosome. This Entry Consists Of The 60s Subunit Of The First 80s In The Asymmetric Unit.

+

+ Sequence ID: pdb|3O58|1 + Length: 3396 + Number of Matches: 5 +

+
+ + + See 2 more title(s) + + + + +
+

+ Range 1: 2959 to 2967 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
18.3 bits(9)11.99/9(100%)0/9(0%)Plus/Plus
+ +
Query        4  CCGTCGTGA  12
+                |||||||||
+Subject   2959  CCGTCGTGA  2967
+
+
+

+ Range 2: 1634 to 1627 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
16.4 bits(8)47.08/8(100%)0/8(0%)Plus/Minus
+ +
Query        8  CGTGAAGA  15
+                ||||||||
+Subject   1634  CGTGAAGA  1627
+
+
+

+ Range 3: 2435 to 2442 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
16.4 bits(8)47.08/8(100%)0/8(0%)Plus/Plus
+ +
Query        9  GTGAAGAG  16
+                ||||||||
+Subject   2435  GTGAAGAG  2442
+
+
+

+ Range 4: 1100 to 1106 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query       10  TGAAGAG  16
+                |||||||
+Subject   1100  TGAAGAG  1106
+
+
+

+ Range 5: 2216 to 2222 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query        9  GTGAAGA  15
+                |||||||
+Subject   2216  GTGAAGA  2222
+
+ +
+ +
+ + + +
+

Chain 1, Yeast 80s Ribosome. This Entry Consists Of The 60s Subunit Of The Second 80s In The Asymmetric Unit.

+

+ Sequence ID: pdb|3O5H|1 + Length: 3396 + Number of Matches: 5 +

+
+ + + See 2 more title(s) + + + + +
+

+ Range 1: 2959 to 2967 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
18.3 bits(9)11.99/9(100%)0/9(0%)Plus/Plus
+ +
Query        4  CCGTCGTGA  12
+                |||||||||
+Subject   2959  CCGTCGTGA  2967
+
+
+

+ Range 2: 1634 to 1627 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
16.4 bits(8)47.08/8(100%)0/8(0%)Plus/Minus
+ +
Query        8  CGTGAAGA  15
+                ||||||||
+Subject   1634  CGTGAAGA  1627
+
+
+

+ Range 3: 2435 to 2442 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
16.4 bits(8)47.08/8(100%)0/8(0%)Plus/Plus
+ +
Query        9  GTGAAGAG  16
+                ||||||||
+Subject   2435  GTGAAGAG  2442
+
+
+

+ Range 4: 1100 to 1106 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query       10  TGAAGAG  16
+                |||||||
+Subject   1100  TGAAGAG  1106
+
+
+

+ Range 5: 2216 to 2222 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query        9  GTGAAGA  15
+                |||||||
+Subject   2216  GTGAAGA  2222
+
+ +
+ +
+ + + +
+

Chain 1, Yeast 80s Ribosome. This Entry Consists Of The 40s Subunit Of The First 80s In The Asymmetric Unit.

+

+ Sequence ID: pdb|3O2Z|1 + Length: 1800 + Number of Matches: 3 +

+
+ + +
+

+ Range 1: 1528 to 1536 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
18.3 bits(9)11.99/9(100%)0/9(0%)Plus/Plus
+ +
Query        3  TCCGTCGTG  11
+                |||||||||
+Subject   1528  TCCGTCGTG  1536
+
+
+

+ Range 2: 1006 to 1012 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query        4  CCGTCGT  10
+                |||||||
+Subject   1006  CCGTCGT  1012
+
+
+

+ Range 3: 1569 to 1563 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Minus
+ +
Query       10  TGAAGAG  16
+                |||||||
+Subject   1569  TGAAGAG  1563
+
+ +
+ +
+ + + +
+

Chain 1, Yeast 80s Ribosome. This Entry Consists Of The 40s Subunit Of The Second 80s In The Asymmetric Unit.

+

+ Sequence ID: pdb|3O30|1 + Length: 1800 + Number of Matches: 3 +

+
+ + +
+

+ Range 1: 1528 to 1536 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
18.3 bits(9)11.99/9(100%)0/9(0%)Plus/Plus
+ +
Query        3  TCCGTCGTG  11
+                |||||||||
+Subject   1528  TCCGTCGTG  1536
+
+
+

+ Range 2: 1006 to 1012 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query        4  CCGTCGT  10
+                |||||||
+Subject   1006  CCGTCGT  1012
+
+
+

+ Range 3: 1569 to 1563 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Minus
+ +
Query       10  TGAAGAG  16
+                |||||||
+Subject   1569  TGAAGAG  1563
+
+ +
+ +
+ + + +
+

Chain A, Model Of The Large Subunit Rna Based On A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae Translating 80s Ribosome (With Es27l-In Conformation)

+

+ Sequence ID: pdb|3IZF|A + Length: 3396 + Number of Matches: 5 +

+
+ + +
+

+ Range 1: 2959 to 2967 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
18.3 bits(9)11.99/9(100%)0/9(0%)Plus/Plus
+ +
Query        4  CCGTCGTGA  12
+                |||||||||
+Subject   2959  CCGTCGTGA  2967
+
+
+

+ Range 2: 1634 to 1627 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
16.4 bits(8)47.08/8(100%)0/8(0%)Plus/Minus
+ +
Query        8  CGTGAAGA  15
+                ||||||||
+Subject   1634  CGTGAAGA  1627
+
+
+

+ Range 3: 2435 to 2442 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
16.4 bits(8)47.08/8(100%)0/8(0%)Plus/Plus
+ +
Query        9  GTGAAGAG  16
+                ||||||||
+Subject   2435  GTGAAGAG  2442
+
+
+

+ Range 4: 1100 to 1106 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query       10  TGAAGAG  16
+                |||||||
+Subject   1100  TGAAGAG  1106
+
+
+

+ Range 5: 2216 to 2222 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query        9  GTGAAGA  15
+                |||||||
+Subject   2216  GTGAAGA  2222
+
+ +
+ +
+ + + +
+

Chain A, Model Of The Small Subunit Rna Based On A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae Translating 80s Ribosome

+

+ Sequence ID: pdb|3IZE|A + Length: 1800 + Number of Matches: 3 +

+
+ + +
+

+ Range 1: 1528 to 1536 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
18.3 bits(9)11.99/9(100%)0/9(0%)Plus/Plus
+ +
Query        3  TCCGTCGTG  11
+                |||||||||
+Subject   1528  TCCGTCGTG  1536
+
+
+

+ Range 2: 1006 to 1012 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query        4  CCGTCGT  10
+                |||||||
+Subject   1006  CCGTCGT  1012
+
+
+

+ Range 3: 1569 to 1563 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Minus
+ +
Query       10  TGAAGAG  16
+                |||||||
+Subject   1569  TGAAGAG  1563
+
+ +
+ +
+ + + +
+

Chain I, I-Msoi Re-Designed For Altered Dna Cleavage Specificity (-7c)

+

+ Sequence ID: pdb|3KO2|I + Length: 24 + Number of Matches: 1 +

+
+ + +
+

+ Range 1: 19 to 11 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
18.3 bits(9)11.99/9(100%)0/9(0%)Plus/Minus
+ +
Query        4  CCGTCGTGA  12
+                |||||||||
+Subject     19  CCGTCGTGA  11
+
+ +
+ +
+ + + +
+

Chain H, I-Msoi Re-Designed For Altered Dna Cleavage Specificity (-7c)

+

+ Sequence ID: pdb|3KO2|H + Length: 24 + Number of Matches: 1 +

+
+ + +
+

+ Range 1: 6 to 14 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
18.3 bits(9)11.99/9(100%)0/9(0%)Plus/Plus
+ +
Query        4  CCGTCGTGA  12
+                |||||||||
+Subject      6  CCGTCGTGA  14
+
+ +
+ +
+ + + +
+

Chain D, I-Msoi Re-Designed For Altered Dna Cleavage Specificity (-7c)

+

+ Sequence ID: pdb|3KO2|D + Length: 24 + Number of Matches: 1 +

+
+ + +
+

+ Range 1: 19 to 11 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
18.3 bits(9)11.99/9(100%)0/9(0%)Plus/Minus
+ +
Query        4  CCGTCGTGA  12
+                |||||||||
+Subject     19  CCGTCGTGA  11
+
+ +
+ +
+ + + +
+

Chain C, I-Msoi Re-Designed For Altered Dna Cleavage Specificity (-7c)

+

+ Sequence ID: pdb|3KO2|C + Length: 24 + Number of Matches: 1 +

+
+ + +
+

+ Range 1: 6 to 14 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
18.3 bits(9)11.99/9(100%)0/9(0%)Plus/Plus
+ +
Query        4  CCGTCGTGA  12
+                |||||||||
+Subject      6  CCGTCGTGA  14
+
+ +
+ +
+ + + +
+

Chain 0, Co-Crystal Structure Of Triacetyloleandomcyin Bound To The Large Ribosomal Subunit

+

+ Sequence ID: pdb|3I56|0 + Length: 2923 + Number of Matches: 3 +

+
+ + +
+

+ Range 1: 305 to 297 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
18.3 bits(9)11.99/9(100%)0/9(0%)Plus/Minus
+ +
Query        7  TCGTGAAGA  15
+                |||||||||
+Subject    305  TCGTGAAGA  297
+
+
+

+ Range 2: 2625 to 2633 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
18.3 bits(9)11.99/9(100%)0/9(0%)Plus/Plus
+ +
Query        4  CCGTCGTGA  12
+                |||||||||
+Subject   2625  CCGTCGTGA  2633
+
+
+

+ Range 3: 2606 to 2612 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query        6  GTCGTGA  12
+                |||||||
+Subject   2606  GTCGTGA  2612
+
+ +
+ +
+ + + +
+

Chain 5, Structure Of The 60s Rrna For Eukaryotic Ribosome Based On Cryo-Em Map Of Thermomyces Lanuginosus Ribosome At 8.9a Resolution

+

+ Sequence ID: pdb|3JYX|5 + Length: 3170 + Number of Matches: 5 +

+
+ + +
+

+ Range 1: 2740 to 2748 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
18.3 bits(9)11.99/9(100%)0/9(0%)Plus/Plus
+ +
Query        4  CCGTCGTGA  12
+                |||||||||
+Subject   2740  CCGTCGTGA  2748
+
+
+

+ Range 2: 1587 to 1580 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
16.4 bits(8)47.08/8(100%)0/8(0%)Plus/Minus
+ +
Query        8  CGTGAAGA  15
+                ||||||||
+Subject   1587  CGTGAAGA  1580
+
+
+

+ Range 3: 2222 to 2229 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
16.4 bits(8)47.08/8(100%)0/8(0%)Plus/Plus
+ +
Query        9  GTGAAGAG  16
+                ||||||||
+Subject   2222  GTGAAGAG  2229
+
+
+

+ Range 4: 1344 to 1350 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query        6  GTCGTGA  12
+                |||||||
+Subject   1344  GTCGTGA  1350
+
+
+

+ Range 5: 2003 to 2009 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query        9  GTGAAGA  15
+                |||||||
+Subject   2003  GTGAAGA  2009
+
+ +
+ +
+ + + +
+

Chain A, Structure Of The 40s Rrna And Proteins And PE TRNA FOR EUKARYOTIC Ribosome Based On Cryo-Em Map Of Thermomyces Lanuginosus Ribosome At 8.9a Resolution

+

+ Sequence ID: pdb|3JYV|A + Length: 1761 + Number of Matches: 3 +

+
+ + +
+

+ Range 1: 1492 to 1500 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
18.3 bits(9)11.99/9(100%)0/9(0%)Plus/Plus
+ +
Query        3  TCCGTCGTG  11
+                |||||||||
+Subject   1492  TCCGTCGTG  1500
+
+
+

+ Range 2: 981 to 987 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query        4  CCGTCGT  10
+                |||||||
+Subject    981  CCGTCGT  987
+
+
+

+ Range 3: 1533 to 1527 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Minus
+ +
Query       10  TGAAGAG  16
+                |||||||
+Subject   1533  TGAAGAG  1527
+
+ +
+ +
+ + + +
+

Chain 3, Structure Of The Ribosomal 80s-Eef2-Sordarin Complex From Yeast Obtained By Docking Atomic Models For Rna And Protein Components Into A 11.7 A Cryo-Em Map. This File, 1s1i, Contains 60s Subunit. The 40s Ribosomal Subunit Is In File 1s1h.

+

+ Sequence ID: pdb|1S1I|3 + Length: 2999 + Number of Matches: 2 +

+
+ + +
+

+ Range 1: 2710 to 2718 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
18.3 bits(9)11.99/9(100%)0/9(0%)Plus/Plus
+ +
Query        4  CCGTCGTGA  12
+                |||||||||
+Subject   2710  CCGTCGTGA  2718
+
+
+

+ Range 2: 2691 to 2697 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query        6  GTCGTGA  12
+                |||||||
+Subject   2691  GTCGTGA  2697
+
+ +
+ +
+ + + +
+

Chain 0, Negamycin Binds To The Wall Of The Nascent Chain Exit Tunnel Of The 50s Ribosomal Subunit

+

+ Sequence ID: pdb|2QEX|0 + Length: 2772 + Number of Matches: 2 +

+
+ + +
+

+ Range 1: 2476 to 2484 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
18.3 bits(9)11.99/9(100%)0/9(0%)Plus/Plus
+ +
Query        4  CCGTCGTGA  12
+                |||||||||
+Subject   2476  CCGTCGTGA  2484
+
+
+

+ Range 2: 2457 to 2463 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query        6  GTCGTGA  12
+                |||||||
+Subject   2457  GTCGTGA  2463
+
+ +
+ +
+ + + +
+

Chain 0, The Structure Of The Antibiotic Linezolid Bound To The Large Ribosomal Subunit Of Haloarcula Marismortui

+

+ Sequence ID: pdb|3CPW|0 + Length: 2922 + Number of Matches: 2 +

+
+ + +
+

+ Range 1: 2624 to 2632 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
18.3 bits(9)11.99/9(100%)0/9(0%)Plus/Plus
+ +
Query        4  CCGTCGTGA  12
+                |||||||||
+Subject   2624  CCGTCGTGA  2632
+
+
+

+ Range 2: 2605 to 2611 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query        6  GTCGTGA  12
+                |||||||
+Subject   2605  GTCGTGA  2611
+
+ +
+ +
+ + + +
+

Chain 0, Structure Of Anisomycin Resistant 50s Ribosomal Subunit: 23s Rrna Mutation G2616a

+

+ Sequence ID: pdb|3CCV|0 + Length: 2923 + Number of Matches: 3 +

+
+ + + See 1 more title(s) + + + + +
+

+ Range 1: 305 to 297 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
18.3 bits(9)11.99/9(100%)0/9(0%)Plus/Minus
+ +
Query        7  TCGTGAAGA  15
+                |||||||||
+Subject    305  TCGTGAAGA  297
+
+
+

+ Range 2: 2625 to 2633 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
18.3 bits(9)11.99/9(100%)0/9(0%)Plus/Plus
+ +
Query        4  CCGTCGTGA  12
+                |||||||||
+Subject   2625  CCGTCGTGA  2633
+
+
+

+ Range 3: 2606 to 2612 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query        6  GTCGTGA  12
+                |||||||
+Subject   2606  GTCGTGA  2612
+
+ +
+ +
+ + + +
+

Chain 0, Structure Of Anisomycin Resistant 50s Ribosomal Subunit: 23s Rrna Mutation G2482c

+

+ Sequence ID: pdb|3CCU|0 + Length: 2923 + Number of Matches: 3 +

+
+ + +
+

+ Range 1: 305 to 297 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
18.3 bits(9)11.99/9(100%)0/9(0%)Plus/Minus
+ +
Query        7  TCGTGAAGA  15
+                |||||||||
+Subject    305  TCGTGAAGA  297
+
+
+

+ Range 2: 2625 to 2633 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
18.3 bits(9)11.99/9(100%)0/9(0%)Plus/Plus
+ +
Query        4  CCGTCGTGA  12
+                |||||||||
+Subject   2625  CCGTCGTGA  2633
+
+
+

+ Range 3: 2606 to 2612 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query        6  GTCGTGA  12
+                |||||||
+Subject   2606  GTCGTGA  2612
+
+ +
+ +
+ + + +
+

Chain 0, Structure Of Anisomycin Resistant 50s Ribosomal Subunit: 23s Rrna Mutation G2482a

+

+ Sequence ID: pdb|3CCS|0 + Length: 2923 + Number of Matches: 3 +

+
+ + +
+

+ Range 1: 305 to 297 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
18.3 bits(9)11.99/9(100%)0/9(0%)Plus/Minus
+ +
Query        7  TCGTGAAGA  15
+                |||||||||
+Subject    305  TCGTGAAGA  297
+
+
+

+ Range 2: 2625 to 2633 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
18.3 bits(9)11.99/9(100%)0/9(0%)Plus/Plus
+ +
Query        4  CCGTCGTGA  12
+                |||||||||
+Subject   2625  CCGTCGTGA  2633
+
+
+

+ Range 3: 2606 to 2612 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query        6  GTCGTGA  12
+                |||||||
+Subject   2606  GTCGTGA  2612
+
+ +
+ +
+ + + +
+

Chain 0, Structure Of Anisomycin Resistant 50s Ribosomal Subunit: 23s Rrna Mutation A2488c. Density For Anisomycin Is Visible But Not Included In The Model.

+

+ Sequence ID: pdb|3CCR|0 + Length: 2923 + Number of Matches: 3 +

+
+ + +
+

+ Range 1: 305 to 297 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
18.3 bits(9)11.99/9(100%)0/9(0%)Plus/Minus
+ +
Query        7  TCGTGAAGA  15
+                |||||||||
+Subject    305  TCGTGAAGA  297
+
+
+

+ Range 2: 2625 to 2633 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
18.3 bits(9)11.99/9(100%)0/9(0%)Plus/Plus
+ +
Query        4  CCGTCGTGA  12
+                |||||||||
+Subject   2625  CCGTCGTGA  2633
+
+
+

+ Range 3: 2606 to 2612 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query        6  GTCGTGA  12
+                |||||||
+Subject   2606  GTCGTGA  2612
+
+ +
+ +
+ + + +
+

Chain 0, Structure Of Anisomycin Resistant 50s Ribosomal Subunit: 23s Rrna Mutation A2488u

+

+ Sequence ID: pdb|3CCQ|0 + Length: 2923 + Number of Matches: 3 +

+
+ + +
+

+ Range 1: 305 to 297 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
18.3 bits(9)11.99/9(100%)0/9(0%)Plus/Minus
+ +
Query        7  TCGTGAAGA  15
+                |||||||||
+Subject    305  TCGTGAAGA  297
+
+
+

+ Range 2: 2625 to 2633 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
18.3 bits(9)11.99/9(100%)0/9(0%)Plus/Plus
+ +
Query        4  CCGTCGTGA  12
+                |||||||||
+Subject   2625  CCGTCGTGA  2633
+
+
+

+ Range 3: 2606 to 2612 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query        6  GTCGTGA  12
+                |||||||
+Subject   2606  GTCGTGA  2612
+
+ +
+ +
+ + + +
+

Chain 0, Structure Of Anisomycin Resistant 50s Ribosomal Subunit: 23s Rrna Mutation G2611u

+

+ Sequence ID: pdb|3CCM|0 + Length: 2923 + Number of Matches: 2 +

+
+ + +
+

+ Range 1: 305 to 297 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
18.3 bits(9)11.99/9(100%)0/9(0%)Plus/Minus
+ +
Query        7  TCGTGAAGA  15
+                |||||||||
+Subject    305  TCGTGAAGA  297
+
+
+

+ Range 2: 2625 to 2633 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
18.3 bits(9)11.99/9(100%)0/9(0%)Plus/Plus
+ +
Query        4  CCGTCGTGA  12
+                |||||||||
+Subject   2625  CCGTCGTGA  2633
+
+ +
+ +
+ + + +
+

Chain 0, Structure Of Anisomycin Resistant 50s Ribosomal Subunit: 23s Rrna Mutation U2535c. Density For Anisomycin Is Visible But Not Included In Model.

+

+ Sequence ID: pdb|3CCL|0 + Length: 2923 + Number of Matches: 3 +

+
+ + +
+

+ Range 1: 305 to 297 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
18.3 bits(9)11.99/9(100%)0/9(0%)Plus/Minus
+ +
Query        7  TCGTGAAGA  15
+                |||||||||
+Subject    305  TCGTGAAGA  297
+
+
+

+ Range 2: 2625 to 2633 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
18.3 bits(9)11.99/9(100%)0/9(0%)Plus/Plus
+ +
Query        4  CCGTCGTGA  12
+                |||||||||
+Subject   2625  CCGTCGTGA  2633
+
+
+

+ Range 3: 2606 to 2612 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query        6  GTCGTGA  12
+                |||||||
+Subject   2606  GTCGTGA  2612
+
+ +
+ +
+ + + +
+

Chain 0, Structure Of Anisomycin Resistant 50s Ribosomal Subunit: 23s Rrna Mutation C2534u

+

+ Sequence ID: pdb|3CCJ|0 + Length: 2923 + Number of Matches: 3 +

+
+ + +
+

+ Range 1: 305 to 297 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
18.3 bits(9)11.99/9(100%)0/9(0%)Plus/Minus
+ +
Query        7  TCGTGAAGA  15
+                |||||||||
+Subject    305  TCGTGAAGA  297
+
+
+

+ Range 2: 2625 to 2633 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
18.3 bits(9)11.99/9(100%)0/9(0%)Plus/Plus
+ +
Query        4  CCGTCGTGA  12
+                |||||||||
+Subject   2625  CCGTCGTGA  2633
+
+
+

+ Range 3: 2606 to 2612 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query        6  GTCGTGA  12
+                |||||||
+Subject   2606  GTCGTGA  2612
+
+ +
+ +
+ + + +
+

Chain 0, Structure Of Anisomycin Resistant 50s Ribosomal Subunit: 23s Rrna Mutation U2535a

+

+ Sequence ID: pdb|3CCE|0 + Length: 2923 + Number of Matches: 3 +

+
+ + +
+

+ Range 1: 305 to 297 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
18.3 bits(9)11.99/9(100%)0/9(0%)Plus/Minus
+ +
Query        7  TCGTGAAGA  15
+                |||||||||
+Subject    305  TCGTGAAGA  297
+
+
+

+ Range 2: 2625 to 2633 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
18.3 bits(9)11.99/9(100%)0/9(0%)Plus/Plus
+ +
Query        4  CCGTCGTGA  12
+                |||||||||
+Subject   2625  CCGTCGTGA  2633
+
+
+

+ Range 3: 2606 to 2612 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query        6  GTCGTGA  12
+                |||||||
+Subject   2606  GTCGTGA  2612
+
+ +
+ +
+ + + +
+

Chain 0, Structure Of Anisomycin Resistant 50s Ribosomal Subunit: 23s Rrna Mutation C2487u

+

+ Sequence ID: pdb|3CC7|0 + Length: 2923 + Number of Matches: 3 +

+
+ + +
+

+ Range 1: 305 to 297 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
18.3 bits(9)11.99/9(100%)0/9(0%)Plus/Minus
+ +
Query        7  TCGTGAAGA  15
+                |||||||||
+Subject    305  TCGTGAAGA  297
+
+
+

+ Range 2: 2625 to 2633 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
18.3 bits(9)11.99/9(100%)0/9(0%)Plus/Plus
+ +
Query        4  CCGTCGTGA  12
+                |||||||||
+Subject   2625  CCGTCGTGA  2633
+
+
+

+ Range 3: 2606 to 2612 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query        6  GTCGTGA  12
+                |||||||
+Subject   2606  GTCGTGA  2612
+
+ +
+ +
+ + + +
+

Chain 0, The Refined Crystal Structure Of The Haloarcula Marismortui Large Ribosomal Subunit At 2.4 Angstrom Resolution With Rrna Sequence For The 23s Rrna And Genome-Derived Sequences For R-Proteins

+

+ Sequence ID: pdb|3CC2|0 + Length: 2923 + Number of Matches: 3 +

+
+ + + See 7 more title(s) + + + + +
+

+ Range 1: 305 to 297 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
18.3 bits(9)11.99/9(100%)0/9(0%)Plus/Minus
+ +
Query        7  TCGTGAAGA  15
+                |||||||||
+Subject    305  TCGTGAAGA  297
+
+
+

+ Range 2: 2625 to 2633 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
18.3 bits(9)11.99/9(100%)0/9(0%)Plus/Plus
+ +
Query        4  CCGTCGTGA  12
+                |||||||||
+Subject   2625  CCGTCGTGA  2633
+
+
+

+ Range 3: 2606 to 2612 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query        6  GTCGTGA  12
+                |||||||
+Subject   2606  GTCGTGA  2612
+
+ +
+ +
+ + + +
+

Chain 0, Structure Of A Mammalian Ribosomal 60s Subunit Within An 80s Complex Obtained By Docking Homology Models Of The Rna And Proteins Into An 8.7 A Cryo-Em Map

+

+ Sequence ID: pdb|2ZKR|0 + Length: 2903 + Number of Matches: 4 +

+
+ + +
+

+ Range 1: 2623 to 2631 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
18.3 bits(9)11.99/9(100%)0/9(0%)Plus/Plus
+ +
Query        4  CCGTCGTGA  12
+                |||||||||
+Subject   2623  CCGTCGTGA  2631
+
+
+

+ Range 2: 2111 to 2118 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
16.4 bits(8)47.08/8(100%)0/8(0%)Plus/Plus
+ +
Query        9  GTGAAGAG  16
+                ||||||||
+Subject   2111  GTGAAGAG  2118
+
+
+

+ Range 3: 353 to 359 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query       10  TGAAGAG  16
+                |||||||
+Subject    353  TGAAGAG  359
+
+
+

+ Range 4: 1892 to 1898 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query        9  GTGAAGA  15
+                |||||||
+Subject   1892  GTGAAGA  1898
+
+ +
+ +
+ + + +
+

Chain 0, A More Complete Structure Of The The L7L12 STALK OF THE Haloarcula Marismortui 50s Large Ribosomal Subunit

+

+ Sequence ID: pdb|2QA4|0 + Length: 2922 + Number of Matches: 2 +

+
+ + +
+

+ Range 1: 2624 to 2632 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
18.3 bits(9)11.99/9(100%)0/9(0%)Plus/Plus
+ +
Query        4  CCGTCGTGA  12
+                |||||||||
+Subject   2624  CCGTCGTGA  2632
+
+
+

+ Range 2: 2605 to 2611 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query        6  GTCGTGA  12
+                |||||||
+Subject   2605  GTCGTGA  2611
+
+ +
+ +
+ + + +
+

Chain R, Structural Model For The Large Subunit Of The Mammalian Mitochondrial Ribosome

+

+ Sequence ID: pdb|2FTC|R + Length: 1568 + Number of Matches: 1 +

+
+ + +
+

+ Range 1: 1032 to 1040 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
18.3 bits(9)11.99/9(100%)0/9(0%)Plus/Plus
+ +
Query        8  CGTGAAGAG  16
+                |||||||||
+Subject   1032  CGTGAAGAG  1040
+
+ +
+ +
+ + + +
+

Chain 0, Refined Crystal Structure Of The Haloarcula Marismortui Large Ribosomal Subunit At 2.4 Angstrom Resolution

+

+ Sequence ID: pdb|1S72|0 + Length: 2922 + Number of Matches: 2 +

+
+ + + See 14 more title(s) + + + + +
+

+ Range 1: 2624 to 2632 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
18.3 bits(9)11.99/9(100%)0/9(0%)Plus/Plus
+ +
Query        4  CCGTCGTGA  12
+                |||||||||
+Subject   2624  CCGTCGTGA  2632
+
+
+

+ Range 2: 2605 to 2611 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query        6  GTCGTGA  12
+                |||||||
+Subject   2605  GTCGTGA  2611
+
+ +
+ +
+ + + +
+

Chain 0, Crystal Structure Of Virginiamycin M And S Bound To The 50s Ribosomal Subunit Of Haloarcula Marismortui

+

+ Sequence ID: pdb|1YIT|0 + Length: 2922 + Number of Matches: 3 +

+
+ + + See 1 more title(s) + + + + +
+

+ Range 1: 305 to 297 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
18.3 bits(9)11.99/9(100%)0/9(0%)Plus/Minus
+ +
Query        7  TCGTGAAGA  15
+                |||||||||
+Subject    305  TCGTGAAGA  297
+
+
+

+ Range 2: 2625 to 2633 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
18.3 bits(9)11.99/9(100%)0/9(0%)Plus/Plus
+ +
Query        4  CCGTCGTGA  12
+                |||||||||
+Subject   2625  CCGTCGTGA  2633
+
+
+

+ Range 3: 2606 to 2612 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query        6  GTCGTGA  12
+                |||||||
+Subject   2606  GTCGTGA  2612
+
+ +
+ +
+ + + +
+

Chain 0, Crystal Structure Of Azithromycin Bound To The G2099a Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui

+

+ Sequence ID: pdb|1YHQ|0 + Length: 2922 + Number of Matches: 3 +

+
+ + + See 3 more title(s) + + + + +
+

+ Range 1: 305 to 297 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
18.3 bits(9)11.99/9(100%)0/9(0%)Plus/Minus
+ +
Query        7  TCGTGAAGA  15
+                |||||||||
+Subject    305  TCGTGAAGA  297
+
+
+

+ Range 2: 2625 to 2633 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
18.3 bits(9)11.99/9(100%)0/9(0%)Plus/Plus
+ +
Query        4  CCGTCGTGA  12
+                |||||||||
+Subject   2625  CCGTCGTGA  2633
+
+
+

+ Range 3: 2606 to 2612 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query        6  GTCGTGA  12
+                |||||||
+Subject   2606  GTCGTGA  2612
+
+ +
+ +
+ + + +
+

Chain 0, Crystal Structure Of Quinupristin Bound To The G2099a Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui

+

+ Sequence ID: pdb|1YJW|0 + Length: 2922 + Number of Matches: 3 +

+
+ + +
+

+ Range 1: 305 to 297 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
18.3 bits(9)11.99/9(100%)0/9(0%)Plus/Minus
+ +
Query        7  TCGTGAAGA  15
+                |||||||||
+Subject    305  TCGTGAAGA  297
+
+
+

+ Range 2: 2625 to 2633 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
18.3 bits(9)11.99/9(100%)0/9(0%)Plus/Plus
+ +
Query        4  CCGTCGTGA  12
+                |||||||||
+Subject   2625  CCGTCGTGA  2633
+
+
+

+ Range 3: 2606 to 2612 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query        6  GTCGTGA  12
+                |||||||
+Subject   2606  GTCGTGA  2612
+
+ +
+ +
+ + + +
+

Chain A, Crystal Structure Of Cca-Phe-Cap-Biotin Bound Simultaneously At Half Occupancy To Both The A-Site And P- Site Of The The 50s Ribosomal Subunit.

+

+ Sequence ID: pdb|1Q86|A + Length: 2922 + Number of Matches: 2 +

+
+ + +
+

+ Range 1: 2624 to 2632 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
18.3 bits(9)11.99/9(100%)0/9(0%)Plus/Plus
+ +
Query        4  CCGTCGTGA  12
+                |||||||||
+Subject   2624  CCGTCGTGA  2632
+
+
+

+ Range 2: 2605 to 2611 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query        6  GTCGTGA  12
+                |||||||
+Subject   2605  GTCGTGA  2611
+
+ +
+ +
+ + + +
+

Chain 0, Fully Refined Crystal Structure Of The Haloarcula Marismortui Large Ribosomal Subunit At 2.4 Angstrom Resolution

+

+ Sequence ID: pdb|1JJ2|0 + Length: 2922 + Number of Matches: 2 +

+
+ + + See 16 more title(s) + + + + +
+

+ Range 1: 2624 to 2632 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
18.3 bits(9)11.99/9(100%)0/9(0%)Plus/Plus
+ +
Query        4  CCGTCGTGA  12
+                |||||||||
+Subject   2624  CCGTCGTGA  2632
+
+
+

+ Range 2: 2605 to 2611 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query        6  GTCGTGA  12
+                |||||||
+Subject   2605  GTCGTGA  2611
+
+ +
+ +
+ + + +
+

Chain A, Co-Crystal Structure Of Blasticidin S Bound To The 50s Ribosomal Subunit

+

+ Sequence ID: pdb|1KC8|A + Length: 2922 + Number of Matches: 2 +

+
+ + +
+

+ Range 1: 2624 to 2632 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
18.3 bits(9)11.99/9(100%)0/9(0%)Plus/Plus
+ +
Query        4  CCGTCGTGA  12
+                |||||||||
+Subject   2624  CCGTCGTGA  2632
+
+
+

+ Range 2: 2605 to 2611 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query        6  GTCGTGA  12
+                |||||||
+Subject   2605  GTCGTGA  2611
+
+ +
+ +
+ + + +
+

Chain 0, Crystal Structure Of The Large Ribosomal Subunit From Haloarcula Marismortui At 2.4 Angstrom Resolution

+

+ Sequence ID: pdb|1FFK|0 + Length: 2922 + Number of Matches: 2 +

+
+ + +
+

+ Range 1: 2624 to 2632 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
18.3 bits(9)11.99/9(100%)0/9(0%)Plus/Plus
+ +
Query        4  CCGTCGTGA  12
+                |||||||||
+Subject   2624  CCGTCGTGA  2632
+
+
+

+ Range 2: 2605 to 2611 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query        6  GTCGTGA  12
+                |||||||
+Subject   2605  GTCGTGA  2611
+
+ +
+ +
+ + + +
+

Chain A, Large Ribosomal Subunit Complexed With A 13 Bp Minihelix- Puromycin Compound

+

+ Sequence ID: pdb|1FG0|A + Length: 602 + Number of Matches: 2 +

+
+ + +
+

+ Range 1: 563 to 571 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
18.3 bits(9)11.99/9(100%)0/9(0%)Plus/Plus
+ +
Query        4  CCGTCGTGA  12
+                |||||||||
+Subject    563  CCGTCGTGA  571
+
+
+

+ Range 2: 544 to 550 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query        6  GTCGTGA  12
+                |||||||
+Subject    544  GTCGTGA  550
+
+ +
+ +
+ + + +
+

Chain A, Large Ribosomal Subunit Complexed With R(Cc)-Da-Puromycin

+

+ Sequence ID: pdb|1FFZ|A + Length: 602 + Number of Matches: 2 +

+
+ + +
+

+ Range 1: 563 to 571 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
18.3 bits(9)11.99/9(100%)0/9(0%)Plus/Plus
+ +
Query        4  CCGTCGTGA  12
+                |||||||||
+Subject    563  CCGTCGTGA  571
+
+
+

+ Range 2: 544 to 550 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query        6  GTCGTGA  12
+                |||||||
+Subject    544  GTCGTGA  550
+
+ +
+ +
+ + + +
+

Chain F, Crystal Structure Of The Catalytic Domain Of Rlub In Complex With A 21-nucleotide Rna Substrate

+

+ Sequence ID: pdb|4LGT|F + Length: 21 + Number of Matches: 1 +

+
+ + +
+

+ Range 1: 5 to 12 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
16.4 bits(8)47.08/8(100%)0/8(0%)Plus/Plus
+ +
Query        5  CGTCGTGA  12
+                ||||||||
+Subject      5  CGTCGTGA  12
+
+ +
+ +
+ + + +
+

Chain E, Crystal Structure Of The Catalytic Domain Of Rlub In Complex With A 21-nucleotide Rna Substrate

+

+ Sequence ID: pdb|4LGT|E + Length: 21 + Number of Matches: 1 +

+
+ + +
+

+ Range 1: 5 to 12 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
16.4 bits(8)47.08/8(100%)0/8(0%)Plus/Plus
+ +
Query        5  CGTCGTGA  12
+                ||||||||
+Subject      5  CGTCGTGA  12
+
+ +
+ +
+ + + +
+

Chain A, Thermus Thermophilus Ribosome

+

+ Sequence ID: pdb|4BTD|A + Length: 2915 + Number of Matches: 2 +

+
+ + +
+

+ Range 1: 2048 to 2055 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
16.4 bits(8)47.08/8(100%)0/8(0%)Plus/Plus
+ +
Query        8  CGTGAAGA  15
+                ||||||||
+Subject   2048  CGTGAAGA  2055
+
+
+

+ Range 2: 2603 to 2610 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
16.4 bits(8)47.08/8(100%)0/8(0%)Plus/Plus
+ +
Query        5  CGTCGTGA  12
+                ||||||||
+Subject   2603  CGTCGTGA  2610
+
+ +
+ +
+ + + +
+

Chain A, Crystal Structure Of Blasticidin S Bound To Thermus Thermophilus 70s Ribosome. This File Contains The 50s Subunit And Blasticidin S Molecule From The First 70s Ribosome.

+

+ Sequence ID: pdb|4L6J|A + Length: 2879 + Number of Matches: 2 +

+
+ + + See 1 more title(s) + + + + +
+

+ Range 1: 2021 to 2028 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
16.4 bits(8)47.08/8(100%)0/8(0%)Plus/Plus
+ +
Query        8  CGTGAAGA  15
+                ||||||||
+Subject   2021  CGTGAAGA  2028
+
+
+

+ Range 2: 2576 to 2583 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
16.4 bits(8)47.08/8(100%)0/8(0%)Plus/Plus
+ +
Query        5  CGTCGTGA  12
+                ||||||||
+Subject   2576  CGTCGTGA  2583
+
+ +
+ +
+ + + +
+

Chain A, Crystal Structure Of The 70s Ribosome Bound With The Q253p Mutant Of Release Factor Rf2. 50s Of The A Subunit

+

+ Sequence ID: pdb|4KFI|A + Length: 2879 + Number of Matches: 2 +

+
+ + + See 1 more title(s) + + + + +
+

+ Range 1: 2021 to 2028 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
16.4 bits(8)47.08/8(100%)0/8(0%)Plus/Plus
+ +
Query        8  CGTGAAGA  15
+                ||||||||
+Subject   2021  CGTGAAGA  2028
+
+
+

+ Range 2: 2576 to 2583 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
16.4 bits(8)47.08/8(100%)0/8(0%)Plus/Plus
+ +
Query        5  CGTCGTGA  12
+                ||||||||
+Subject   2576  CGTCGTGA  2583
+
+ +
+ +
+ + + +
+

Chain A, Crystal Structure Of Thermus Thermophilus 70s Containing Trnas And Mrna Stop Codon With Pseudouridine

+

+ Sequence ID: pdb|4K0Q|A + Length: 2915 + Number of Matches: 2 +

+
+ + +
+

+ Range 1: 2048 to 2055 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
16.4 bits(8)47.08/8(100%)0/8(0%)Plus/Plus
+ +
Query        8  CGTGAAGA  15
+                ||||||||
+Subject   2048  CGTGAAGA  2055
+
+
+

+ Range 2: 2603 to 2610 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
16.4 bits(8)47.08/8(100%)0/8(0%)Plus/Plus
+ +
Query        5  CGTCGTGA  12
+                ||||||||
+Subject   2603  CGTCGTGA  2610
+
+ +
+ +
+ + + +
+

Chain A, Crystal Structure Of Thermus Thermophilus 70s Containing Trnas And Mrna Stop Codon With Pseudouridine

+

+ Sequence ID: pdb|4K0M|A + Length: 2915 + Number of Matches: 2 +

+
+ + +
+

+ Range 1: 2048 to 2055 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
16.4 bits(8)47.08/8(100%)0/8(0%)Plus/Plus
+ +
Query        8  CGTGAAGA  15
+                ||||||||
+Subject   2048  CGTGAAGA  2055
+
+
+

+ Range 2: 2603 to 2610 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
16.4 bits(8)47.08/8(100%)0/8(0%)Plus/Plus
+ +
Query        5  CGTCGTGA  12
+                ||||||||
+Subject   2603  CGTCGTGA  2610
+
+ +
+ +
+ + + +
+

Chain A, Atomic Model Of The Immature 50s Subunit From Bacillus Subtilis (state I-a)

+

+ Sequence ID: pdb|3J3V|A + Length: 2927 + Number of Matches: 5 +

+
+ + +
+

+ Range 1: 2620 to 2627 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
16.4 bits(8)47.08/8(100%)0/8(0%)Plus/Plus
+ +
Query        5  CGTCGTGA  12
+                ||||||||
+Subject   2620  CGTCGTGA  2627
+
+
+

+ Range 2: 340 to 346 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query       10  TGAAGAG  16
+                |||||||
+Subject    340  TGAAGAG  346
+
+
+

+ Range 3: 440 to 446 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query        3  TCCGTCG  9
+                |||||||
+Subject    440  TCCGTCG  446
+
+
+

+ Range 4: 2056 to 2062 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query        9  GTGAAGA  15
+                |||||||
+Subject   2056  GTGAAGA  2062
+
+
+

+ Range 5: 2644 to 2650 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query        3  TCCGTCG  9
+                |||||||
+Subject   2644  TCCGTCG  2650
+
+ +
+ +
+ + + +
+

Chain A, Atomic Model Of The Immature 50s Subunit From Bacillus Subtilis (state Ii-a)

+

+ Sequence ID: pdb|3J3W|A + Length: 2927 + Number of Matches: 5 +

+
+ + +
+

+ Range 1: 2620 to 2627 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
16.4 bits(8)47.08/8(100%)0/8(0%)Plus/Plus
+ +
Query        5  CGTCGTGA  12
+                ||||||||
+Subject   2620  CGTCGTGA  2627
+
+
+

+ Range 2: 340 to 346 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query       10  TGAAGAG  16
+                |||||||
+Subject    340  TGAAGAG  346
+
+
+

+ Range 3: 440 to 446 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query        3  TCCGTCG  9
+                |||||||
+Subject    440  TCCGTCG  446
+
+
+

+ Range 4: 2056 to 2062 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query        9  GTGAAGA  15
+                |||||||
+Subject   2056  GTGAAGA  2062
+
+
+

+ Range 5: 2644 to 2650 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query        3  TCCGTCG  9
+                |||||||
+Subject   2644  TCCGTCG  2650
+
+ +
+ +
+ + + +
+

Chain A, Crystal Structure Of The Bacterial Ribosome Ram Mutation G347u. This Entry Contains The 50s Ribosomal Subunit Of The Second 70s Molecule In The Asymmetric Unit

+

+ Sequence ID: pdb|3V6X|A + Length: 2916 + Number of Matches: 2 +

+
+ + +
+

+ Range 1: 2048 to 2055 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
16.4 bits(8)47.08/8(100%)0/8(0%)Plus/Plus
+ +
Query        8  CGTGAAGA  15
+                ||||||||
+Subject   2048  CGTGAAGA  2055
+
+
+

+ Range 2: 2603 to 2610 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
16.4 bits(8)47.08/8(100%)0/8(0%)Plus/Plus
+ +
Query        5  CGTCGTGA  12
+                ||||||||
+Subject   2603  CGTCGTGA  2610
+
+ +
+ +
+ + + +
+

Chain A, Crystal Structure Of The Bacterial Ribosome Ram Mutation G347u. This Entry Contains The 50s Ribosomal Subunit Of The First 70s Molecule In The Asymmetric Unit

+

+ Sequence ID: pdb|3V6W|A + Length: 2916 + Number of Matches: 2 +

+
+ + +
+

+ Range 1: 2048 to 2055 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
16.4 bits(8)47.08/8(100%)0/8(0%)Plus/Plus
+ +
Query        8  CGTGAAGA  15
+                ||||||||
+Subject   2048  CGTGAAGA  2055
+
+
+

+ Range 2: 2603 to 2610 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
16.4 bits(8)47.08/8(100%)0/8(0%)Plus/Plus
+ +
Query        5  CGTCGTGA  12
+                ||||||||
+Subject   2603  CGTCGTGA  2610
+
+ +
+ +
+ + + +
+

Chain d, The Cryo-Em Structure Of A 3d Dna-Origami Object

+

+ Sequence ID: pdb|2YMI|DD + Length: 56 + Number of Matches: 1 +

+
+ + +
+

+ Range 1: 52 to 45 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
16.4 bits(8)47.08/8(100%)0/8(0%)Plus/Minus
+ +
Query        5  CGTCGTGA  12
+                ||||||||
+Subject     52  CGTCGTGA  45
+
+ +
+ +
+ + + +
+

Chain A, The Cryo-Em Structure Of A 3d Dna-Origami Object

+

+ Sequence ID: pdb|2YMF|A + Length: 4896 + Number of Matches: 2 +

+
+ + +
+

+ Range 1: 575 to 582 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
16.4 bits(8)47.08/8(100%)0/8(0%)Plus/Plus
+ +
Query        5  CGTCGTGA  12
+                ||||||||
+Subject    575  CGTCGTGA  582
+
+
+

+ Range 2: 561 to 567 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
14.4 bits(7)185.87/7(100%)0/7(0%)Plus/Plus
+ +
Query        4  CCGTCGT  10
+                |||||||
+Subject    561  CCGTCGT  567
+
+ +
+ +
+ + + +
+

Chain A, Structure Of The Thermus Thermophilus 70s Ribosome Complexed With Mrna, Trna And Paromomycin (Part 2 Of 4). This File Contains The 50s Subunit From Molecule I.

+

+ Sequence ID: pdb|2J01|A + Length: 2787 + Number of Matches: 2 +

+
+ + + See 1 more title(s) + + + + +
+

+ Range 1: 1948 to 1955 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
16.4 bits(8)47.08/8(100%)0/8(0%)Plus/Plus
+ +
Query        8  CGTGAAGA  15
+                ||||||||
+Subject   1948  CGTGAAGA  1955
+
+
+

+ Range 2: 2474 to 2481 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
16.4 bits(8)47.08/8(100%)0/8(0%)Plus/Plus
+ +
Query        5  CGTCGTGA  12
+                ||||||||
+Subject   2474  CGTCGTGA  2481
+
+ +
+ +
+ + + +
+

Chain C, Crystal Structure Of I-Crei Complexed With Its Target Methylated At Position Plus 2 (In The B Strand) In The Presence Of Magnesium

+

+ Sequence ID: pdb|4AQX|C + Length: 14 + Number of Matches: 1 +

+
+ + +
+

+ Range 1: 7 to 14 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
16.4 bits(8)47.08/8(100%)0/8(0%)Plus/Plus
+ +
Query        5  CGTCGTGA  12
+                ||||||||
+Subject      7  CGTCGTGA  14
+
+ +
+ +
+ + + +
+

Chain C, Crystal Structure Of I-Crei Complexed With Its Target Methylated At Position Plus 2 (In The B Strand) In The Presence Of Calcium

+

+ Sequence ID: pdb|4AQU|C + Length: 24 + Number of Matches: 1 +

+
+ + +
+

+ Range 1: 7 to 14 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
16.4 bits(8)47.08/8(100%)0/8(0%)Plus/Plus
+ +
Query        5  CGTCGTGA  12
+                ||||||||
+Subject      7  CGTCGTGA  14
+
+ +
+ +
+
+
+ +
+ + + + + diff -r 000000000000 -r a54279222d84 test-data/blast xml example1.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/blast xml example1.xml Mon May 19 09:43:54 2014 -0400 @@ -0,0 +1,6548 @@ + + + + blastn + BLASTN 2.2.29+ + Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. + pdb + 106397 + No definition line + 16 + + + 1000 + 1 + -3 + 5 + 2 + F + + + + + 1 + 106397 + No definition line + 16 + + + 1 + gi|557804730|pdb|3J5K|A + Chain A, E. Coli 70s-fmetval-trnaval Post-translocation Complex (post4, 50s Subunit) + 3J5K_A + 2903 + + + 1 + 32.2105 + 16 + 0.000791334 + 1 + 16 + 961 + 976 + 1 + 1 + 16 + 16 + 0 + 16 + CGTCCGTCGTGAAGAG + CGTCCGTCGTGAAGAG + |||||||||||||||| + + + 2 + 16.3517 + 8 + 47.0266 + 5 + 12 + 2591 + 2598 + 1 + 1 + 8 + 8 + 0 + 8 + CGTCGTGA + CGTCGTGA + |||||||| + + + 3 + 14.3694 + 7 + 185.82 + 7 + 13 + 839 + 845 + 1 + 1 + 7 + 7 + 0 + 7 + TCGTGAA + TCGTGAA + ||||||| + + + 4 + 14.3694 + 7 + 185.82 + 9 + 15 + 2027 + 2033 + 1 + 1 + 7 + 7 + 0 + 7 + GTGAAGA + GTGAAGA + ||||||| + + + + + 2 + gi|557804675|pdb|3J5I|A + Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Intermediate Post- Translocation State (post3b, 50s Subunit) + 3J5I_A + 2903 + + + 1 + 32.2105 + 16 + 0.000791334 + 1 + 16 + 961 + 976 + 1 + 1 + 16 + 16 + 0 + 16 + CGTCCGTCGTGAAGAG + CGTCCGTCGTGAAGAG + |||||||||||||||| + + + 2 + 16.3517 + 8 + 47.0266 + 5 + 12 + 2591 + 2598 + 1 + 1 + 8 + 8 + 0 + 8 + CGTCGTGA + CGTCGTGA + |||||||| + + + 3 + 14.3694 + 7 + 185.82 + 7 + 13 + 839 + 845 + 1 + 1 + 7 + 7 + 0 + 7 + TCGTGAA + TCGTGAA + ||||||| + + + 4 + 14.3694 + 7 + 185.82 + 9 + 15 + 2027 + 2033 + 1 + 1 + 7 + 7 + 0 + 7 + GTGAAGA + GTGAAGA + ||||||| + + + + + 3 + gi|557804619|pdb|3J5G|A + Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Intermediate Post- Translocation State (post3a, 50s Subunit) + 3J5G_A + 2903 + + + 1 + 32.2105 + 16 + 0.000791334 + 1 + 16 + 961 + 976 + 1 + 1 + 16 + 16 + 0 + 16 + CGTCCGTCGTGAAGAG + CGTCCGTCGTGAAGAG + |||||||||||||||| + + + 2 + 16.3517 + 8 + 47.0266 + 5 + 12 + 2591 + 2598 + 1 + 1 + 8 + 8 + 0 + 8 + CGTCGTGA + CGTCGTGA + |||||||| + + + 3 + 14.3694 + 7 + 185.82 + 7 + 13 + 839 + 845 + 1 + 1 + 7 + 7 + 0 + 7 + TCGTGAA + TCGTGAA + ||||||| + + + 4 + 14.3694 + 7 + 185.82 + 9 + 15 + 2027 + 2033 + 1 + 1 + 7 + 7 + 0 + 7 + GTGAAGA + GTGAAGA + ||||||| + + + + + 4 + gi|557804563|pdb|3J5E|A + Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Intermediate Post- Translocation State (post2b, 50s Subunit) + 3J5E_A + 2903 + + + 1 + 32.2105 + 16 + 0.000791334 + 1 + 16 + 961 + 976 + 1 + 1 + 16 + 16 + 0 + 16 + CGTCCGTCGTGAAGAG + CGTCCGTCGTGAAGAG + |||||||||||||||| + + + 2 + 16.3517 + 8 + 47.0266 + 5 + 12 + 2591 + 2598 + 1 + 1 + 8 + 8 + 0 + 8 + CGTCGTGA + CGTCGTGA + |||||||| + + + 3 + 14.3694 + 7 + 185.82 + 7 + 13 + 839 + 845 + 1 + 1 + 7 + 7 + 0 + 7 + TCGTGAA + TCGTGAA + ||||||| + + + 4 + 14.3694 + 7 + 185.82 + 9 + 15 + 2027 + 2033 + 1 + 1 + 7 + 7 + 0 + 7 + GTGAAGA + GTGAAGA + ||||||| + + + + + 5 + gi|557804507|pdb|3J5C|A + Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Intermediate Post- Translocation State (post2a, 50s Subunit) + 3J5C_A + 2903 + + + 1 + 32.2105 + 16 + 0.000791334 + 1 + 16 + 961 + 976 + 1 + 1 + 16 + 16 + 0 + 16 + CGTCCGTCGTGAAGAG + CGTCCGTCGTGAAGAG + |||||||||||||||| + + + 2 + 16.3517 + 8 + 47.0266 + 5 + 12 + 2591 + 2598 + 1 + 1 + 8 + 8 + 0 + 8 + CGTCGTGA + CGTCGTGA + |||||||| + + + 3 + 14.3694 + 7 + 185.82 + 7 + 13 + 839 + 845 + 1 + 1 + 7 + 7 + 0 + 7 + TCGTGAA + TCGTGAA + ||||||| + + + 4 + 14.3694 + 7 + 185.82 + 9 + 15 + 2027 + 2033 + 1 + 1 + 7 + 7 + 0 + 7 + GTGAAGA + GTGAAGA + ||||||| + + + + + 6 + gi|557804451|pdb|3J5A|A + Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Classic Post- Translocation State (post1, 50s Subunit) + 3J5A_A + 2903 + + + 1 + 32.2105 + 16 + 0.000791334 + 1 + 16 + 961 + 976 + 1 + 1 + 16 + 16 + 0 + 16 + CGTCCGTCGTGAAGAG + CGTCCGTCGTGAAGAG + |||||||||||||||| + + + 2 + 16.3517 + 8 + 47.0266 + 5 + 12 + 2591 + 2598 + 1 + 1 + 8 + 8 + 0 + 8 + CGTCGTGA + CGTCGTGA + |||||||| + + + 3 + 14.3694 + 7 + 185.82 + 7 + 13 + 839 + 845 + 1 + 1 + 7 + 7 + 0 + 7 + TCGTGAA + TCGTGAA + ||||||| + + + 4 + 14.3694 + 7 + 185.82 + 9 + 15 + 2027 + 2033 + 1 + 1 + 7 + 7 + 0 + 7 + GTGAAGA + GTGAAGA + ||||||| + + + + + 7 + gi|557804395|pdb|3J58|A + Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Hybrid Pre- Translocation State (pre5b, 50s Subunit) + 3J58_A + 2903 + + + 1 + 32.2105 + 16 + 0.000791334 + 1 + 16 + 961 + 976 + 1 + 1 + 16 + 16 + 0 + 16 + CGTCCGTCGTGAAGAG + CGTCCGTCGTGAAGAG + |||||||||||||||| + + + 2 + 16.3517 + 8 + 47.0266 + 5 + 12 + 2591 + 2598 + 1 + 1 + 8 + 8 + 0 + 8 + CGTCGTGA + CGTCGTGA + |||||||| + + + 3 + 14.3694 + 7 + 185.82 + 7 + 13 + 839 + 845 + 1 + 1 + 7 + 7 + 0 + 7 + TCGTGAA + TCGTGAA + ||||||| + + + 4 + 14.3694 + 7 + 185.82 + 9 + 15 + 2027 + 2033 + 1 + 1 + 7 + 7 + 0 + 7 + GTGAAGA + GTGAAGA + ||||||| + + + + + 8 + gi|557804339|pdb|3J56|A + Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Hybrid Pre- Translocation State (pre5a, 50s Subunit) + 3J56_A + 2903 + + + 1 + 32.2105 + 16 + 0.000791334 + 1 + 16 + 961 + 976 + 1 + 1 + 16 + 16 + 0 + 16 + CGTCCGTCGTGAAGAG + CGTCCGTCGTGAAGAG + |||||||||||||||| + + + 2 + 16.3517 + 8 + 47.0266 + 5 + 12 + 2591 + 2598 + 1 + 1 + 8 + 8 + 0 + 8 + CGTCGTGA + CGTCGTGA + |||||||| + + + 3 + 14.3694 + 7 + 185.82 + 7 + 13 + 839 + 845 + 1 + 1 + 7 + 7 + 0 + 7 + TCGTGAA + TCGTGAA + ||||||| + + + 4 + 14.3694 + 7 + 185.82 + 9 + 15 + 2027 + 2033 + 1 + 1 + 7 + 7 + 0 + 7 + GTGAAGA + GTGAAGA + ||||||| + + + + + 9 + gi|557804283|pdb|3J54|A + Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Hybrid Pre- Translocation State (pre4, 50s Subunit) + 3J54_A + 2903 + + + 1 + 32.2105 + 16 + 0.000791334 + 1 + 16 + 961 + 976 + 1 + 1 + 16 + 16 + 0 + 16 + CGTCCGTCGTGAAGAG + CGTCCGTCGTGAAGAG + |||||||||||||||| + + + 2 + 16.3517 + 8 + 47.0266 + 5 + 12 + 2591 + 2598 + 1 + 1 + 8 + 8 + 0 + 8 + CGTCGTGA + CGTCGTGA + |||||||| + + + 3 + 14.3694 + 7 + 185.82 + 7 + 13 + 839 + 845 + 1 + 1 + 7 + 7 + 0 + 7 + TCGTGAA + TCGTGAA + ||||||| + + + 4 + 14.3694 + 7 + 185.82 + 9 + 15 + 2027 + 2033 + 1 + 1 + 7 + 7 + 0 + 7 + GTGAAGA + GTGAAGA + ||||||| + + + + + 10 + gi|557804227|pdb|3J52|A + Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Classic Pre- Translocation State (pre1a, 50s Subunit) + 3J52_A + 2903 + + + 1 + 32.2105 + 16 + 0.000791334 + 1 + 16 + 961 + 976 + 1 + 1 + 16 + 16 + 0 + 16 + CGTCCGTCGTGAAGAG + CGTCCGTCGTGAAGAG + |||||||||||||||| + + + 2 + 16.3517 + 8 + 47.0266 + 5 + 12 + 2591 + 2598 + 1 + 1 + 8 + 8 + 0 + 8 + CGTCGTGA + CGTCGTGA + |||||||| + + + 3 + 14.3694 + 7 + 185.82 + 7 + 13 + 839 + 845 + 1 + 1 + 7 + 7 + 0 + 7 + TCGTGAA + TCGTGAA + ||||||| + + + 4 + 14.3694 + 7 + 185.82 + 9 + 15 + 2027 + 2033 + 1 + 1 + 7 + 7 + 0 + 7 + GTGAAGA + GTGAAGA + ||||||| + + + + + 11 + gi|557804195|pdb|3J51|A + Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Intermediate Pre- Translocation State (pre3, 50s Subunit) + 3J51_A + 2903 + + + 1 + 32.2105 + 16 + 0.000791334 + 1 + 16 + 961 + 976 + 1 + 1 + 16 + 16 + 0 + 16 + CGTCCGTCGTGAAGAG + CGTCCGTCGTGAAGAG + |||||||||||||||| + + + 2 + 16.3517 + 8 + 47.0266 + 5 + 12 + 2591 + 2598 + 1 + 1 + 8 + 8 + 0 + 8 + CGTCGTGA + CGTCGTGA + |||||||| + + + 3 + 14.3694 + 7 + 185.82 + 7 + 13 + 839 + 845 + 1 + 1 + 7 + 7 + 0 + 7 + TCGTGAA + TCGTGAA + ||||||| + + + 4 + 14.3694 + 7 + 185.82 + 9 + 15 + 2027 + 2033 + 1 + 1 + 7 + 7 + 0 + 7 + GTGAAGA + GTGAAGA + ||||||| + + + + + 12 + gi|557804163|pdb|3J50|A + Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Intermediate Pre- Translocation State (pre2, 50s Subunit) + 3J50_A + 2903 + + + 1 + 32.2105 + 16 + 0.000791334 + 1 + 16 + 961 + 976 + 1 + 1 + 16 + 16 + 0 + 16 + CGTCCGTCGTGAAGAG + CGTCCGTCGTGAAGAG + |||||||||||||||| + + + 2 + 16.3517 + 8 + 47.0266 + 5 + 12 + 2591 + 2598 + 1 + 1 + 8 + 8 + 0 + 8 + CGTCGTGA + CGTCGTGA + |||||||| + + + 3 + 14.3694 + 7 + 185.82 + 7 + 13 + 839 + 845 + 1 + 1 + 7 + 7 + 0 + 7 + TCGTGAA + TCGTGAA + ||||||| + + + 4 + 14.3694 + 7 + 185.82 + 9 + 15 + 2027 + 2033 + 1 + 1 + 7 + 7 + 0 + 7 + GTGAAGA + GTGAAGA + ||||||| + + + + + 13 + gi|557804083|pdb|3J4X|A + Chain A, E. Coli 70s-fmetval-trnaval-trnafmet Complex In Classic Pre- Translocation State (pre1b, 50s Subunit) + 3J4X_A + 2903 + + + 1 + 32.2105 + 16 + 0.000791334 + 1 + 16 + 961 + 976 + 1 + 1 + 16 + 16 + 0 + 16 + CGTCCGTCGTGAAGAG + CGTCCGTCGTGAAGAG + |||||||||||||||| + + + 2 + 16.3517 + 8 + 47.0266 + 5 + 12 + 2591 + 2598 + 1 + 1 + 8 + 8 + 0 + 8 + CGTCGTGA + CGTCGTGA + |||||||| + + + 3 + 14.3694 + 7 + 185.82 + 7 + 13 + 839 + 845 + 1 + 1 + 7 + 7 + 0 + 7 + TCGTGAA + TCGTGAA + ||||||| + + + 4 + 14.3694 + 7 + 185.82 + 9 + 15 + 2027 + 2033 + 1 + 1 + 7 + 7 + 0 + 7 + GTGAAGA + GTGAAGA + ||||||| + + + + + 14 + gi|474452808|pdb|3J37|A + Chain A, Tetracycline Resistance Protein Tet(o) Bound To The Ribosome + 3J37_A + 2904 + + + 1 + 32.2105 + 16 + 0.000791334 + 1 + 16 + 961 + 976 + 1 + 1 + 16 + 16 + 0 + 16 + CGTCCGTCGTGAAGAG + CGTCCGTCGTGAAGAG + |||||||||||||||| + + + 2 + 16.3517 + 8 + 47.0266 + 5 + 12 + 2591 + 2598 + 1 + 1 + 8 + 8 + 0 + 8 + CGTCGTGA + CGTCGTGA + |||||||| + + + 3 + 14.3694 + 7 + 185.82 + 7 + 13 + 839 + 845 + 1 + 1 + 7 + 7 + 0 + 7 + TCGTGAA + TCGTGAA + ||||||| + + + + + 15 + gi|326634210|pdb|3IZT|B + Chain B, Structural Insights Into Cognate Vs. Near-Cognate Discrimination During Decoding. This Entry Contains The Large Subunit Of A Ribosome Programmed With A Near-Cognate Codon. >gi|326634243|pdb|3IZU|B Chain B, Structural Insights Into Cognate Vs. Near-Cognate Discrimination During Decoding. This Entry Contains The Large Subunit Of A Ribosome Programmed With A Cognate Codon >gi|380763703|pdb|3J0T|B Chain B, Structural Characterization Of Mrna-Trna Translocation Intermediates (50s Ribosome Of Class2 Of The Six Classes) >gi|380763785|pdb|3J0W|B Chain B, Structural Characterization Of Mrna-Trna Translocation Intermediates (50s Ribosome Of Class 4a Of The Six Classes) >gi|380763843|pdb|3J0Y|B Chain B, Structural Characterization Of Mrna-Trna Translocation Intermediates (50s Ribosome Of Class 4b Of The Six Classes) >gi|380763925|pdb|3J11|B Chain B, Structural Characterization Of Mrna-Trna Translocation Intermediates (50s Ribosome Of Class 3 Of The Six Classes) >gi|380763959|pdb|3J12|B Chain B, Structural Characterization Of Mrna-Trna Translocation Intermediates (50s Ribosome Of Class 5 Of The Six Classes) >gi|380764016|pdb|3J14|B Chain B, Structural Characterization Of Mrna-Trna Translocation Intermediates (50s Ribosome Of Class 6 Of The Six Classes) + 3IZT_B + 2904 + + + 1 + 32.2105 + 16 + 0.000791334 + 1 + 16 + 961 + 976 + 1 + 1 + 16 + 16 + 0 + 16 + CGTCCGTCGTGAAGAG + CGTCCGTCGTGAAGAG + |||||||||||||||| + + + 2 + 16.3517 + 8 + 47.0266 + 5 + 12 + 2591 + 2598 + 1 + 1 + 8 + 8 + 0 + 8 + CGTCGTGA + CGTCGTGA + |||||||| + + + 3 + 14.3694 + 7 + 185.82 + 7 + 13 + 839 + 845 + 1 + 1 + 7 + 7 + 0 + 7 + TCGTGAA + TCGTGAA + ||||||| + + + + + 16 + gi|224510767|pdb|3FIK|B + Chain B, Ternary Complex-Bound E.Coli 70s Ribosome. This Entry Consists Of The 50s Subunit. >gi|257097373|pdb|3I1N|A Chain A, Crystal Structure Of The E. Coli 70s Ribosome In An Intermediate State Of Ratcheting >gi|257097425|pdb|3I1P|A Chain A, Crystal Structure Of The E. Coli 70s Ribosome In An Intermediate State Of Ratcheting >gi|257097479|pdb|3I1R|A Chain A, Crystal Structure Of The E. Coli 70s Ribosome In An Intermediate State Of Ratcheting >gi|257097533|pdb|3I1T|A Chain A, Crystal Structure Of The E. Coli 70s Ribosome In An Intermediate State Of Ratcheting >gi|257097588|pdb|3I20|A Chain A, Crystal Structure Of The E. Coli 70s Ribosome In An Intermediate State Of Ratcheting >gi|257097643|pdb|3I22|A Chain A, Crystal Structure Of The E. Coli 70s Ribosome In An Intermediate State Of Ratcheting >gi|294662251|pdb|2WWQ|B Chain B, E.Coli 70s Ribosome Stalled During Translation Of Tnac Leader Peptide. This File Contains The 50s, The P-Site Trna And The Tnac Leader Peptide (Part 2 Of 2). >gi|309320065|pdb|3OFC|A Chain A, Crystal Structure Of The E. Coli Ribosome Bound To Chloramphenicol. This File Contains The 50s Subunit Of The First 70s Ribosome With Chloramphenicol Bound. >gi|309320169|pdb|3OFZ|A Chain A, Crystal Structure Of The E. Coli Ribosome Bound To Clindamycin. This File Contains The 50s Subunit Of The First 70s Ribosome Bound To Clindamycin. >gi|309320200|pdb|3OG0|A Chain A, Crystal Structure Of The E. Coli Ribosome Bound To Clindamycin. This File Contains The 50s Subunit Of The Second 70s Ribosome. >gi|315113654|pdb|3OAS|A Chain A, Crystal Structure Of The E. Coli Ribosome Bound To Telithromycin. This File Contains The 50s Subunit Of The Second 70s Ribosome. >gi|315113685|pdb|3OAT|A Chain A, Crystal Structure Of The E. Coli Ribosome Bound To Telithromycin. This File Contains The 50s Subunit Of The First 70s Ribosome With Telithromycin Bound. >gi|334359437|pdb|3R8S|A Chain A, Structures Of The Bacterial Ribosome In Classical And Hybrid States Of Trna Binding >gi|334359468|pdb|3R8T|A Chain A, Structures Of The Bacterial Ribosome In Classical And Hybrid States Of Trna Binding >gi|371927526|pdb|3SGF|A Chain A, Crystal Structure Of Release Factor Rf3 Trapped In The Gtp State On A Rotated Conformation Of The Ribosome >gi|371927651|pdb|3UOS|A Chain A, Crystal Structure Of Release Factor Rf3 Trapped In The Gtp State On A Rotated Conformation Of The Ribosome (Without Viomycin) >gi|386783121|pdb|3J19|A Chain A, Structure Of The Bacterial Ribosome Complexed By Tmrna-Smpb And Ef-G During Translocation And Mld-Loading (50s Subunit) >gi|567754995|pdb|3J5U|A Chain A, Structure Of The Ribosome With Elongation Factor G Trapped In The Pre- Translocation State (pre-translocation 70s*trna Structure, 50s Subunit) >gi|567755029|pdb|3J5W|A Chain A, Structure Of The Ribosome With Elongation Factor G Trapped In The Pre- Translocation State (pre-translocation 70s*trna*ef-g Structure, 50s Subunit) + 3FIK_B + 2903 + + + 1 + 32.2105 + 16 + 0.000791334 + 1 + 16 + 961 + 976 + 1 + 1 + 16 + 16 + 0 + 16 + CGTCCGTCGTGAAGAG + CGTCCGTCGTGAAGAG + |||||||||||||||| + + + 2 + 16.3517 + 8 + 47.0266 + 5 + 12 + 2591 + 2598 + 1 + 1 + 8 + 8 + 0 + 8 + CGTCGTGA + CGTCGTGA + |||||||| + + + 3 + 14.3694 + 7 + 185.82 + 7 + 13 + 839 + 845 + 1 + 1 + 7 + 7 + 0 + 7 + TCGTGAA + TCGTGAA + ||||||| + + + 4 + 14.3694 + 7 + 185.82 + 9 + 15 + 2027 + 2033 + 1 + 1 + 7 + 7 + 0 + 7 + GTGAAGA + GTGAAGA + ||||||| + + + + + 17 + gi|256032374|pdb|3E1B|B + Chain B, Structure Of The 50s Subunit Of E. Coli Ribosome In Pre-Accommodation State >gi|256032431|pdb|3E1D|B Chain B, Structure Of The 50s Subunit Of E. Coli Ribosome In Post-Accommodation State + 3E1B_B + 2903 + + + 1 + 32.2105 + 16 + 0.000791334 + 1 + 16 + 961 + 976 + 1 + 1 + 16 + 16 + 0 + 16 + CGTCCGTCGTGAAGAG + CGTCCGTCGTGAAGAG + |||||||||||||||| + + + 2 + 16.3517 + 8 + 47.0266 + 5 + 12 + 2591 + 2598 + 1 + 1 + 8 + 8 + 0 + 8 + CGTCGTGA + CGTCGTGA + |||||||| + + + 3 + 14.3694 + 7 + 185.82 + 7 + 13 + 839 + 845 + 1 + 1 + 7 + 7 + 0 + 7 + TCGTGAA + TCGTGAA + ||||||| + + + 4 + 14.3694 + 7 + 185.82 + 9 + 15 + 2027 + 2033 + 1 + 1 + 7 + 7 + 0 + 7 + GTGAAGA + GTGAAGA + ||||||| + + + + + 18 + gi|157883716|pdb|2GYC|0 + Chain 0, Structure Of The 50s Subunit Of A Secm-Stalled E. Coli Ribosome Complex Obtained By Fitting Atomic Models For Rna And Protein Components Into Cryo-Em Map Emd-1143 + 2GYC_0 + 2740 + + + 1 + 32.2105 + 16 + 0.000791334 + 1 + 16 + 889 + 904 + 1 + 1 + 16 + 16 + 0 + 16 + CGTCCGTCGTGAAGAG + CGTCCGTCGTGAAGAG + |||||||||||||||| + + + 2 + 16.3517 + 8 + 47.0266 + 5 + 12 + 2453 + 2460 + 1 + 1 + 8 + 8 + 0 + 8 + CGTCGTGA + CGTCGTGA + |||||||| + + + 3 + 14.3694 + 7 + 185.82 + 7 + 13 + 776 + 782 + 1 + 1 + 7 + 7 + 0 + 7 + TCGTGAA + TCGTGAA + ||||||| + + + 4 + 14.3694 + 7 + 185.82 + 9 + 15 + 1910 + 1916 + 1 + 1 + 7 + 7 + 0 + 7 + GTGAAGA + GTGAAGA + ||||||| + + + + + 19 + gi|157883710|pdb|2GYA|0 + Chain 0, Structure Of The 50s Subunit Of A Pre-Translocational E. Coli Ribosome Obtained By Fitting Atomic Models For Rna And Protein Components Into Cryo-Em Map Emd-1056 + 2GYA_0 + 2740 + + + 1 + 32.2105 + 16 + 0.000791334 + 1 + 16 + 889 + 904 + 1 + 1 + 16 + 16 + 0 + 16 + CGTCCGTCGTGAAGAG + CGTCCGTCGTGAAGAG + |||||||||||||||| + + + 2 + 16.3517 + 8 + 47.0266 + 5 + 12 + 2453 + 2460 + 1 + 1 + 8 + 8 + 0 + 8 + CGTCGTGA + CGTCGTGA + |||||||| + + + 3 + 14.3694 + 7 + 185.82 + 7 + 13 + 776 + 782 + 1 + 1 + 7 + 7 + 0 + 7 + TCGTGAA + TCGTGAA + ||||||| + + + 4 + 14.3694 + 7 + 185.82 + 9 + 15 + 1910 + 1916 + 1 + 1 + 7 + 7 + 0 + 7 + GTGAAGA + GTGAAGA + ||||||| + + + + + 20 + gi|122922257|pdb|2I2V|B + Chain B, Crystal Structure Of Ribosome With Messenger Rna And The Anticodon Stem-Loop Of P-Site Trna. This File Contains The 50s Subunit Of One 70s Ribosome. The Entire Crystal Structure Contains Two 70s Ribosomes And Is Described In Remark 400. + 2I2V_B + 2904 + + + 1 + 32.2105 + 16 + 0.000791334 + 1 + 16 + 961 + 976 + 1 + 1 + 16 + 16 + 0 + 16 + CGTCCGTCGTGAAGAG + CGTCCGTCGTGAAGAG + |||||||||||||||| + + + 2 + 16.3517 + 8 + 47.0266 + 5 + 12 + 2591 + 2598 + 1 + 1 + 8 + 8 + 0 + 8 + CGTCGTGA + CGTCGTGA + |||||||| + + + 3 + 14.3694 + 7 + 185.82 + 7 + 13 + 839 + 845 + 1 + 1 + 7 + 7 + 0 + 7 + TCGTGAA + TCGTGAA + ||||||| + + + 4 + 14.3694 + 7 + 185.82 + 9 + 15 + 2027 + 2033 + 1 + 1 + 7 + 7 + 0 + 7 + GTGAAGA + GTGAAGA + ||||||| + + + + + 21 + gi|83754062|pdb|2AW4|B + Chain B, Crystal Structure Of The Bacterial Ribosome From Escherichia Coli At 3.5 A Resolution. This File Contains The 50s Subunit Of One 70s Ribosome. The Entire Crystal Structure Contains Two 70s Ribosomes And Is Described In Remark 400. >gi|122922241|pdb|2I2T|B Chain B, Crystal Structure Of Ribosome With Messenger Rna And The Anticodon Stem-Loop Of P-Site Trna. This File Contains The 50s Subunit Of One 70s Ribosome. The Entire Crystal Structure Contains Two 70s Ribosomes And Is Described In Remark 400. >gi|157836046|pdb|2QOV|B Chain B, Crystal Structure Of The Bacterial Ribosome From Escherichia Coli In Complex With Spectinomycin. This File Contains The 50s Subunit Of The First 70s Ribosome. The Entire Crystal Structure Contains Two 70s Ribosomes. >gi|157836098|pdb|2QOX|B Chain B, Crystal Structure Of The Bacterial Ribosome From Escherichia Coli In Complex With Spectinomycin. This File Contains The 50s Subunit Of The Second 70s Ribosome. The Entire Crystal Structure Contains Two 70s Ribosomes. >gi|157836150|pdb|2QOZ|B Chain B, Crystal Structure Of The Bacterial Ribosome From Escherichia Coli In Complex With Spectinomycin And Neomycin. This File Contains The 50s Subunit Of The First 70s Ribosome, With Neomycin Bound. The Entire Crystal Structure Contains Two 70s Ribosomes. >gi|157836202|pdb|2QP1|B Chain B, Crystal Structure Of The Bacterial Ribosome From Escherichia Coli In Complex With Spectinomycin And Neomycin. This File Contains The 50s Subunit Of The Second 70s Ribosome, With Neomycin Bound. The Entire Crystal Structure Contains Two 70s Ribosomes. >gi|158429721|pdb|2QAM|B Chain B, Crystal Structure Of The Bacterial Ribosome From Escherichia Coli In Complex With Neomycin. This File Contains The 50s Subunit Of The First 70s Ribosome, With Neomycin Bound. The Entire Crystal Structure Contains Two 70s Ribosomes And Is Described In Remark 400. >gi|158429773|pdb|2QAO|B Chain B, Crystal Structure Of The Bacterial Ribosome From Escherichia Coli In Complex With Neomycin. This File Contains The 50s Subunit Of The Second 70s Ribosome, With Neomycin Bound. The Entire Crystal Structure Contains Two 70s Ribosomes And Is Described In Remark 400. >gi|158429831|pdb|2QBA|B Chain B, Crystal Structure Of The Bacterial Ribosome From Escherichia Coli In Complex With Gentamicin. This File Contains The 50s Subunit Of The First 70s Ribosome, With Gentamicin Bound. The Entire Crystal Structure Contains Two 70s Ribosomes And Is Described In Remark 400. >gi|158429883|pdb|2QBC|B Chain B, Crystal Structure Of The Bacterial Ribosome From Escherichia Coli In Complex With Gentamicin. This File Contains The 50s Subunit Of The Second 70s Ribosome, With Gentamicin Bound. The Entire Crystal Structure Contains Two 70s Ribosomes And Is Described In Remark 400. >gi|158429935|pdb|2QBE|B Chain B, Crystal Structure Of The Bacterial Ribosome From Escherichia Coli In Complex With Ribosome Recycling Factor (Rrf). This File Contains The 50s Subunit Of The First 70s Ribosome, With Rrf Bound. The Entire Crystal Structure Contains Two 70s Ribosomes And Is Described In Remark 400. >gi|158429988|pdb|2QBG|B Chain B, Crystal Structure Of The Bacterial Ribosome From Escherichia Coli In Complex With Ribosome Recycling Factor (Rrf). This File Contains The 50s Subunit Of The Second 70s Ribosome, With Rrf Bound. The Entire Crystal Structure Contains Two 70s Ribosomes And Is Described In Remark 400. >gi|158430041|pdb|2QBI|B Chain B, Crystal Structure Of The Bacterial Ribosome From Escherichia Coli In Complex With Gentamicin And Ribosome Recycling Factor (Rrf). This File Contains The 50s Subunit Of The First 70s Ribosome, With Gentamicin And Rrf Bound. The Entire Crystal Structure Contains Two 70s Ribosomes And Is Described In Remark 400. >gi|158430094|pdb|2QBK|B Chain B, Crystal Structure Of The Bacterial Ribosome From Escherichia Coli In Complex With Gentamicin And Ribosome Recycling Factor (Rrf). This File Contains The 50s Subunit Of The Second 70s Ribosome, With Gentamicin And Rrf Bound. The Entire Crystal Structure Contains Two 70s Ribosomes And Is Described In Remark 400. >gi|158431394|pdb|2Z4L|B Chain B, Crystal Structure Of The Bacterial Ribosome From Escherichia Coli In Complex With Paromomycin And Ribosome Recycling Factor (Rrf). This File Contains The 50s Subunit Of The First 70s Ribosome, With Paromomycin And Rrf Bound. The Entire Crystal Structure Contains Two 70s Ribosomes And Is Described In Remark 400. >gi|158431447|pdb|2Z4N|B Chain B, Crystal Structure Of The Bacterial Ribosome From Escherichia Coli In Complex With Paromomycin And Ribosome Recycling Factor (Rrf). This File Contains The 50s Subunit Of The Second 70s Ribosome, With Paromomycin And Rrf Bound. The Entire Crystal Structure Contains Two 70s Ribosomes And Is Described In Remark 400. >gi|168988732|pdb|2VHM|B Chain B, Structure Of Pdf Binding Helix In Complex With The Ribosome (Part 1 Of 4) >gi|168988763|pdb|2VHN|B Chain B, Structure Of Pdf Binding Helix In Complex With The Ribosome. (Part 2 Of 4) >gi|169404603|pdb|2RDO|B Chain B, 50s Subunit With Ef-G(Gdpnp) And Rrf Bound >gi|197107301|pdb|3DF2|B Chain B, Crystal Structure Of The Bacterial Ribosome From Escherichia Coli In Complex With Hygromycin B. This File Contains The 50s Subunit Of The First 70s Ribosome. The Entire Crystal Structure Contains Two 70s Ribosomes. >gi|197107353|pdb|3DF4|B Chain B, Crystal Structure Of The Bacterial Ribosome From Escherichia Coli In Complex With Hygromycin B. This File Contains The 50s Subunit Of The Second 70s Ribosome. The Entire Crystal Structure Contains Two 70s Ribosomes. >gi|290560329|pdb|3KCR|8 Chain 8, Ribosome-Secy Complex. This Entry 3kcr Contains 50s Ribosomal Subnit. The 30s Ribosomal Subunit Can Be Found In Pdb Entry 3kc4 >gi|308198729|pdb|3ORB|A Chain A, Crystal Structure Of The E. Coli Ribosome Bound To Cem-101. This File Contains The 50s Subunit Of The First 70s Ribosome Bound To Cem-101. >gi|308388007|pdb|3OFQ|A Chain A, Crystal Structure Of The E. Coli Ribosome Bound To Erythromycin. This File Contains The 50s Subunit Of The Second 70s Ribosome. >gi|308388038|pdb|3OFR|A Chain A, Crystal Structure Of The E. Coli Ribosome Bound To Erythromycin. This File Contains The 50s Subunit Of The First 70s Ribosome With Erthromycin Bound. >gi|309320096|pdb|3OFD|A Chain A, Crystal Structure Of The E. Coli Ribosome Bound To Chloramphenicol. This File Contains The 50s Subunit Of The Second 70s Ribosome. >gi|329666014|pdb|3J01|8 Chain 8, Structure Of The Ribosome-Secye Complex In The Membrane Environment >gi|402550607|pdb|4GAR|A Chain A, Allosteric Control Of The Ribosome By Small-Molecule Antibiotics >gi|402550662|pdb|4GAU|A Chain A, Allosteric Control Of The Ribosome By Small-Molecule Antibiotics >gi|524934273|pdb|4KIX|A Chain A, Control Of Ribosomal Subunit Rotation By Elongation Factor G >gi|524934341|pdb|4KIZ|A Chain A, Control Of Ribosomal Subunit Rotation By Elongation Factor G >gi|524934404|pdb|4KJ1|A Chain A, Control Of Ribosomal Subunit Rotation By Elongation Factor G >gi|524934483|pdb|4KJ3|A Chain A, Control Of Ribosomal Subunit Rotation By Elongation Factor G >gi|524934551|pdb|4KJ5|A Chain A, Control Of Ribosomal Subunit Rotation By Elongation Factor G >gi|524934613|pdb|4KJ7|A Chain A, Control Of Ribosomal Subunit Rotation By Elongation Factor G >gi|524934678|pdb|4KJ9|A Chain A, Control Of Ribosomal Subunit Rotation By Elongation Factor G >gi|524934740|pdb|4KJB|A Chain A, Control Of Ribosomal Subunit Rotation By Elongation Factor G >gi|564730763|pdb|3J5O|A Chain A, Visualization Of Two Trnas Trapped In Transit During Ef-g-mediated Translocation (50s Subunit) >gi|597959819|pdb|3J5L|A Chain A, Structure Of The E. Coli 50s Subunit With Ermbl Nascent Chain + 2AW4_B + 2904 + + + 1 + 32.2105 + 16 + 0.000791334 + 1 + 16 + 961 + 976 + 1 + 1 + 16 + 16 + 0 + 16 + CGTCCGTCGTGAAGAG + CGTCCGTCGTGAAGAG + |||||||||||||||| + + + 2 + 16.3517 + 8 + 47.0266 + 5 + 12 + 2591 + 2598 + 1 + 1 + 8 + 8 + 0 + 8 + CGTCGTGA + CGTCGTGA + |||||||| + + + 3 + 14.3694 + 7 + 185.82 + 7 + 13 + 839 + 845 + 1 + 1 + 7 + 7 + 0 + 7 + TCGTGAA + TCGTGAA + ||||||| + + + 4 + 14.3694 + 7 + 185.82 + 9 + 15 + 2027 + 2033 + 1 + 1 + 7 + 7 + 0 + 7 + GTGAAGA + GTGAAGA + ||||||| + + + + + 22 + gi|83754118|pdb|2AWB|B + Chain B, Crystal Structure Of The Bacterial Ribosome From Escherichia Coli At 3.5 A Resolution. This File Contains The 50s Subunit Of The Second 70s Ribosome. The Entire Crystal Structure Contains Two 70s Ribosomes And Is Described In Remark 400. >gi|126031747|pdb|2J28|B Chain B, Model Of E. Coli Srp Bound To 70s Rncs >gi|157880574|pdb|1VS8|B Chain B, Crystal Structure Of The Bacterial Ribosome From Escherichia Coli In Complex With The Antibiotic Kasugamyin At 3.5a Resolution. This File Contains The 50s Subunit Of One 70s Ribosome. The Entire Crystal Structure Contains Two 70s Ribosomes And Is Described In Remark 400. + 2AWB_B + 2904 + + + 1 + 32.2105 + 16 + 0.000791334 + 1 + 16 + 961 + 976 + 1 + 1 + 16 + 16 + 0 + 16 + CGTCCGTCGTGAAGAG + CGTCCGTCGTGAAGAG + |||||||||||||||| + + + 2 + 16.3517 + 8 + 47.0266 + 5 + 12 + 2591 + 2598 + 1 + 1 + 8 + 8 + 0 + 8 + CGTCGTGA + CGTCGTGA + |||||||| + + + 3 + 14.3694 + 7 + 185.82 + 7 + 13 + 839 + 845 + 1 + 1 + 7 + 7 + 0 + 7 + TCGTGAA + TCGTGAA + ||||||| + + + 4 + 14.3694 + 7 + 185.82 + 9 + 15 + 2027 + 2033 + 1 + 1 + 7 + 7 + 0 + 7 + GTGAAGA + GTGAAGA + ||||||| + + + + + 23 + gi|157880571|pdb|1VS6|B + Chain B, Crystal Structure Of The Bacterial Ribosome From Escherichia Coli In Complex With The Antibiotic Kasugamyin At 3.5a Resolution. This File Contains The 50s Subunit Of One 70s Ribosome. The Entire Crystal Structure Contains Two 70s Ribosomes And Is Described In Remark 400. >gi|209870354|pdb|3BBX|B Chain B, The Hsp15 Protein Fitted Into The Low Resolution Cryo-Em Map 50s.Nc-Trna.Hsp15 Complex >gi|222447037|pdb|3DG0|B Chain B, Coordinates Of 16s And 23s Rrnas Fitted Into The Cryo-Em Map Of Ef-G-Bound Translocation Complex >gi|222447039|pdb|3DG2|B Chain B, Coordinates Of 16s And 23s Rrnas Fitted Into The Cryo-Em Map Of A Pretranslocation Complex >gi|222447041|pdb|3DG4|B Chain B, Coordinates Of 16s And 23s Rrnas Fitted Into The Cryo-Em Map Of Rf1-Bound Termination Complex >gi|222447043|pdb|3DG5|B Chain B, Coordinates Of 16s And 23s Rrnas Fitted Into The Cryo-Em Map Of Rf3-Bound Termination Complex >gi|308198355|pdb|1VT2|A Chain A, Crystal Structure Of The E. Coli Ribosome Bound To Cem-101. This File Contains The 50s Subunit Of The Second 70s Ribosome. + 1VS6_B + 2904 + + + 1 + 32.2105 + 16 + 0.000791334 + 1 + 16 + 961 + 976 + 1 + 1 + 16 + 16 + 0 + 16 + CGTCCGTCGTGAAGAG + CGTCCGTCGTGAAGAG + |||||||||||||||| + + + 2 + 16.3517 + 8 + 47.0266 + 5 + 12 + 2591 + 2598 + 1 + 1 + 8 + 8 + 0 + 8 + CGTCGTGA + CGTCGTGA + |||||||| + + + 3 + 14.3694 + 7 + 185.82 + 7 + 13 + 839 + 845 + 1 + 1 + 7 + 7 + 0 + 7 + TCGTGAA + TCGTGAA + ||||||| + + + 4 + 14.3694 + 7 + 185.82 + 9 + 15 + 2027 + 2033 + 1 + 1 + 7 + 7 + 0 + 7 + GTGAAGA + GTGAAGA + ||||||| + + + + + 24 + gi|33357900|pdb|1P85|0 + Chain 0, Real Space Refined Coordinates Of The 50s Subunit Fitted Into The Low Resolution Cryo-Em Map Of The Ef-G.Gtp State Of E. Coli 70s Ribosome >gi|33357927|pdb|1P86|0 Chain 0, Real Space Refined Coordinates Of The 50s Subunit Fitted Into The Low Resolution Cryo-Em Map Of The Initiation-Like State Of E. Coli 70s Ribosome + 1P85_0 + 2904 + + + 1 + 32.2105 + 16 + 0.000791334 + 1 + 16 + 961 + 976 + 1 + 1 + 16 + 16 + 0 + 16 + CGTCCGTCGTGAAGAG + CGTCCGTCGTGAAGAG + |||||||||||||||| + + + 2 + 16.3517 + 8 + 47.0266 + 5 + 12 + 2591 + 2598 + 1 + 1 + 8 + 8 + 0 + 8 + CGTCGTGA + CGTCGTGA + |||||||| + + + 3 + 14.3694 + 7 + 185.82 + 7 + 13 + 839 + 845 + 1 + 1 + 7 + 7 + 0 + 7 + TCGTGAA + TCGTGAA + ||||||| + + + 4 + 14.3694 + 7 + 185.82 + 9 + 15 + 2027 + 2033 + 1 + 1 + 7 + 7 + 0 + 7 + GTGAAGA + GTGAAGA + ||||||| + + + + + 25 + gi|7767146|pdb|1C2W|B + Chain B, 23s Rrna Structure Fitted To A Cryo-Electron Microscopic Map At 7.5 Angstroms Resolution + 1C2W_B + 2904 + + + 1 + 26.2635 + 13 + 0.0488207 + 1 + 13 + 961 + 973 + 1 + 1 + 13 + 13 + 0 + 13 + CGTCCGTCGTGAA + CGTCCGTCGTGAA + ||||||||||||| + + + 2 + 14.3694 + 7 + 185.82 + 7 + 13 + 839 + 845 + 1 + 1 + 7 + 7 + 0 + 7 + TCGTGAA + TCGTGAA + ||||||| + + + + + 26 + gi|582044940|pdb|3J62|AA + Chain a, Model Of The Large Subunit Rna Based On A 5.5 A Cryo-em Map Of Triticum Aestivum Translating 80s Ribosome + 3J62_AA + 3391 + + + 1 + 18.3341 + 9 + 11.9013 + 4 + 12 + 2961 + 2969 + 1 + 1 + 9 + 9 + 0 + 9 + CCGTCGTGA + CCGTCGTGA + ||||||||| + + + 2 + 16.3517 + 8 + 47.0266 + 2 + 9 + 177 + 170 + 1 + -1 + 8 + 8 + 0 + 8 + GTCCGTCG + GTCCGTCG + |||||||| + + + 3 + 14.3694 + 7 + 185.82 + 4 + 10 + 553 + 559 + 1 + 1 + 7 + 7 + 0 + 7 + CCGTCGT + CCGTCGT + ||||||| + + + 4 + 14.3694 + 7 + 185.82 + 2 + 8 + 2048 + 2042 + 1 + -1 + 7 + 7 + 0 + 7 + GTCCGTC + GTCCGTC + ||||||| + + + 5 + 14.3694 + 7 + 185.82 + 9 + 15 + 2211 + 2217 + 1 + 1 + 7 + 7 + 0 + 7 + GTGAAGA + GTGAAGA + ||||||| + + + + + 27 + gi|567755268|pdb|4CE4|A + Chain A, 39s Large Subunit Of The Porcine Mitochondrial Ribosome + 4CE4_A + 1570 + + + 1 + 18.3341 + 9 + 11.9013 + 8 + 16 + 1020 + 1028 + 1 + 1 + 9 + 9 + 0 + 9 + CGTGAAGAG + CGTGAAGAG + ||||||||| + + + + + 28 + gi|558704783|pdb|4BYP|5 + Chain 5, Cryo-em Reconstruction Of The 80s-eif5b-met-itrnamet Eukaryotic Translation Initiation Complex + 4BYP_5 + 3396 + + + 1 + 18.3341 + 9 + 11.9013 + 4 + 12 + 2959 + 2967 + 1 + 1 + 9 + 9 + 0 + 9 + CCGTCGTGA + CCGTCGTGA + ||||||||| + + + 2 + 16.3517 + 8 + 47.0266 + 8 + 15 + 1634 + 1627 + 1 + -1 + 8 + 8 + 0 + 8 + CGTGAAGA + CGTGAAGA + |||||||| + + + 3 + 16.3517 + 8 + 47.0266 + 9 + 16 + 2435 + 2442 + 1 + 1 + 8 + 8 + 0 + 8 + GTGAAGAG + GTGAAGAG + |||||||| + + + 4 + 14.3694 + 7 + 185.82 + 10 + 16 + 1100 + 1106 + 1 + 1 + 7 + 7 + 0 + 7 + TGAAGAG + TGAAGAG + ||||||| + + + 5 + 14.3694 + 7 + 185.82 + 9 + 15 + 2216 + 2222 + 1 + 1 + 7 + 7 + 0 + 7 + GTGAAGA + GTGAAGA + ||||||| + + + + + 29 + gi|558704825|pdb|4BYW|5 + Chain 5, Cryo-em Reconstruction Of The 80s-eif5b-met-itrnamet Eukaryotic Translation Initiation Complex + 4BYW_5 + 3396 + + + 1 + 18.3341 + 9 + 11.9013 + 4 + 12 + 2959 + 2967 + 1 + 1 + 9 + 9 + 0 + 9 + CCGTCGTGA + CCGTCGTGA + ||||||||| + + + 2 + 16.3517 + 8 + 47.0266 + 8 + 15 + 1634 + 1627 + 1 + -1 + 8 + 8 + 0 + 8 + CGTGAAGA + CGTGAAGA + |||||||| + + + 3 + 16.3517 + 8 + 47.0266 + 9 + 16 + 2435 + 2442 + 1 + 1 + 8 + 8 + 0 + 8 + GTGAAGAG + GTGAAGAG + |||||||| + + + 4 + 14.3694 + 7 + 185.82 + 10 + 16 + 1100 + 1106 + 1 + 1 + 7 + 7 + 0 + 7 + TGAAGAG + TGAAGAG + ||||||| + + + 5 + 14.3694 + 7 + 185.82 + 9 + 15 + 2216 + 2222 + 1 + 1 + 7 + 7 + 0 + 7 + GTGAAGA + GTGAAGA + ||||||| + + + + + 30 + gi|551701574|pdb|3J44|1 + Chain 1, Structure Of The Methanococcus Jannaschii Ribosome-secyebeta Channel Complex (50s Ribosomal Subunit) + 3J44_1 + 3049 + + + 1 + 18.3341 + 9 + 11.9013 + 1 + 13 + 651 + 663 + 1 + 1 + 12 + 12 + 0 + 13 + CGTCCGTCGTGAA + CGTCCGTCTTGAA + |||||||| |||| + + + 2 + 18.3341 + 9 + 11.9013 + 4 + 12 + 2705 + 2713 + 1 + 1 + 9 + 9 + 0 + 9 + CCGTCGTGA + CCGTCGTGA + ||||||||| + + + + + 31 + gi|508123724|pdb|4HUB|0 + Chain 0, The Re-refined Crystal Structure Of The Haloarcula Marismortui Large Ribosomal Subunit At 2.4 Angstrom Resolution: More Complete Structure Of The L7/l12 And L1 Stalk, L5 And Lx Proteins + 4HUB_0 + 2910 + + + 1 + 18.3341 + 9 + 11.9013 + 7 + 15 + 298 + 290 + 1 + -1 + 9 + 9 + 0 + 9 + TCGTGAAGA + TCGTGAAGA + ||||||||| + + + 2 + 18.3341 + 9 + 11.9013 + 4 + 12 + 2618 + 2626 + 1 + 1 + 9 + 9 + 0 + 9 + CCGTCGTGA + CCGTCGTGA + ||||||||| + + + 3 + 14.3694 + 7 + 185.82 + 6 + 12 + 2599 + 2605 + 1 + 1 + 7 + 7 + 0 + 7 + GTCGTGA + GTCGTGA + ||||||| + + + + + 32 + gi|485601478|pdb|3J3F|5 + Chain 5, Structure Of The H. Sapiens 60s Rrna + 3J3F_5 + 5070 + + + 1 + 18.3341 + 9 + 11.9013 + 4 + 12 + 4536 + 4544 + 1 + 1 + 9 + 9 + 0 + 9 + CCGTCGTGA + CCGTCGTGA + ||||||||| + + + 2 + 16.3517 + 8 + 47.0266 + 1 + 8 + 765 + 772 + 1 + 1 + 8 + 8 + 0 + 8 + CGTCCGTC + CGTCCGTC + |||||||| + + + 3 + 16.3517 + 8 + 47.0266 + 1 + 8 + 769 + 776 + 1 + 1 + 8 + 8 + 0 + 8 + CGTCCGTC + CGTCCGTC + |||||||| + + + 4 + 16.3517 + 8 + 47.0266 + 1 + 8 + 773 + 780 + 1 + 1 + 8 + 8 + 0 + 8 + CGTCCGTC + CGTCCGTC + |||||||| + + + 5 + 16.3517 + 8 + 47.0266 + 1 + 8 + 777 + 784 + 1 + 1 + 8 + 8 + 0 + 8 + CGTCCGTC + CGTCCGTC + |||||||| + + + 6 + 16.3517 + 8 + 47.0266 + 9 + 16 + 3939 + 3946 + 1 + 1 + 8 + 8 + 0 + 8 + GTGAAGAG + GTGAAGAG + |||||||| + + + 7 + 14.3694 + 7 + 185.82 + 10 + 16 + 393 + 399 + 1 + 1 + 7 + 7 + 0 + 7 + TGAAGAG + TGAAGAG + ||||||| + + + 8 + 14.3694 + 7 + 185.82 + 9 + 15 + 3720 + 3726 + 1 + 1 + 7 + 7 + 0 + 7 + GTGAAGA + GTGAAGA + ||||||| + + + + + 33 + gi|485601474|pdb|3J3E|5 + Chain 5, Structure Of The D. Melanogaster 60s Rrna + 3J3E_5 + 3970 + + + 1 + 18.3341 + 9 + 11.9013 + 4 + 12 + 3490 + 3498 + 1 + 1 + 9 + 9 + 0 + 9 + CCGTCGTGA + CCGTCGTGA + ||||||||| + + + 2 + 16.3517 + 8 + 47.0266 + 9 + 16 + 2177 + 2184 + 1 + 1 + 8 + 8 + 0 + 8 + GTGAAGAG + GTGAAGAG + |||||||| + + + 3 + 14.3694 + 7 + 185.82 + 9 + 15 + 2594 + 2600 + 1 + 1 + 7 + 7 + 0 + 7 + GTGAAGA + GTGAAGA + ||||||| + + + 4 + 14.3694 + 7 + 185.82 + 1 + 7 + 3627 + 3633 + 1 + 1 + 7 + 7 + 0 + 7 + CGTCCGT + CGTCCGT + ||||||| + + + + + 34 + gi|449802187|pdb|3ZEX|B + Chain B, High_resolution Cryo-electron Microscopy Structure Of The Trypanosoma Brucei Ribosome + 3ZEX_B + 1465 + + + 1 + 18.3341 + 9 + 11.9013 + 4 + 12 + 1334 + 1342 + 1 + 1 + 9 + 9 + 0 + 9 + CCGTCGTGA + CCGTCGTGA + ||||||||| + + + 2 + 14.3694 + 7 + 185.82 + 10 + 16 + 705 + 711 + 1 + 1 + 7 + 7 + 0 + 7 + TGAAGAG + TGAAGAG + ||||||| + + + + + 35 + gi|428697991|pdb|3J2L|1 + Chain 1, Promiscuous Behavior Of Proteins In Archaeal Ribosomes Revealed By Cryo-em: Implications For Evolution Of Eukaryotic Ribosomes (50s Ribosomal Rna) + 3J2L_1 + 3049 + + + 1 + 18.3341 + 9 + 11.9013 + 1 + 13 + 651 + 663 + 1 + 1 + 12 + 12 + 0 + 13 + CGTCCGTCGTGAA + CGTCCGTCTTGAA + |||||||| |||| + + + 2 + 18.3341 + 9 + 11.9013 + 4 + 12 + 2705 + 2713 + 1 + 1 + 9 + 9 + 0 + 9 + CCGTCGTGA + CCGTCGTGA + ||||||||| + + + + + 36 + gi|392311504|pdb|3OW2|0 + Chain 0, Crystal Structure Of Enhanced Macrolide Bound To 50s Ribosomal Subunit + 3OW2_0 + 2902 + + + 1 + 18.3341 + 9 + 11.9013 + 4 + 12 + 2613 + 2621 + 1 + 1 + 9 + 9 + 0 + 9 + CCGTCGTGA + CCGTCGTGA + ||||||||| + + + 2 + 14.3694 + 7 + 185.82 + 6 + 12 + 2594 + 2600 + 1 + 1 + 7 + 7 + 0 + 7 + GTCGTGA + GTCGTGA + ||||||| + + + + + 37 + gi|374977932|pdb|4ADX|0 + Chain 0, The Cryo-em Structure Of The Archaeal 50s Ribosomal Subunit In Complex With Initiation Factor 6 + 4ADX_0 + 2923 + + + 1 + 18.3341 + 9 + 11.9013 + 7 + 15 + 305 + 297 + 1 + -1 + 9 + 9 + 0 + 9 + TCGTGAAGA + TCGTGAAGA + ||||||||| + + + 2 + 18.3341 + 9 + 11.9013 + 4 + 12 + 2625 + 2633 + 1 + 1 + 9 + 9 + 0 + 9 + CCGTCGTGA + CCGTCGTGA + ||||||||| + + + 3 + 14.3694 + 7 + 185.82 + 6 + 12 + 2606 + 2612 + 1 + 1 + 7 + 7 + 0 + 7 + GTCGTGA + GTCGTGA + ||||||| + + + + + 38 + gi|364506133|pdb|3U5F|6 + Chain 6, The Structure Of The Eukaryotic Ribosome At 3.0 A Resolution. This Entry Contains Ribosomal Rna And Ions Of The 40s Subunit, Ribosome B + 3U5F_6 + 1800 + + + 1 + 18.3341 + 9 + 11.9013 + 3 + 11 + 1528 + 1536 + 1 + 1 + 9 + 9 + 0 + 9 + TCCGTCGTG + TCCGTCGTG + ||||||||| + + + 2 + 14.3694 + 7 + 185.82 + 4 + 10 + 1006 + 1012 + 1 + 1 + 7 + 7 + 0 + 7 + CCGTCGT + CCGTCGT + ||||||| + + + 3 + 14.3694 + 7 + 185.82 + 10 + 16 + 1569 + 1563 + 1 + -1 + 7 + 7 + 0 + 7 + TGAAGAG + TGAAGAG + ||||||| + + + + + 39 + gi|364506095|pdb|3U5B|2 + Chain 2, The Structure Of The Eukaryotic Ribosome At 3.0 A Resolution. This Entry Contains Ribosomal Rna And Ions Of The 40s Subunit, Ribosome A >gi|558704782|pdb|4BYO|2 Chain 2, Cryo-em Reconstruction Of The 80s-eif5b-met-itrnamet Eukaryotic Translation Initiation Complex >gi|558704824|pdb|4BYV|2 Chain 2, Cryo-em Reconstruction Of The 80s-eif5b-met-itrnamet Eukaryotic Translation Initiation Complex + 3U5B_2 + 1800 + + + 1 + 18.3341 + 9 + 11.9013 + 3 + 11 + 1528 + 1536 + 1 + 1 + 9 + 9 + 0 + 9 + TCCGTCGTG + TCCGTCGTG + ||||||||| + + + 2 + 14.3694 + 7 + 185.82 + 4 + 10 + 1006 + 1012 + 1 + 1 + 7 + 7 + 0 + 7 + CCGTCGT + CCGTCGT + ||||||| + + + 3 + 14.3694 + 7 + 185.82 + 10 + 16 + 1569 + 1563 + 1 + -1 + 7 + 7 + 0 + 7 + TGAAGAG + TGAAGAG + ||||||| + + + + + 40 + gi|358440203|pdb|4A1D|1 + Chain 1, T.Thermophila 60s Ribosomal Subunit In Complex With Initiation Factor 6. This File Contains 26s Rrna And Proteins Of Molecule 4. + 4A1D_1 + 3119 + + + 1 + 18.3341 + 9 + 11.9013 + 7 + 15 + 2280 + 2288 + 1 + 1 + 9 + 9 + 0 + 9 + TCGTGAAGA + TCGTGAAGA + ||||||||| + + + 2 + 18.3341 + 9 + 11.9013 + 4 + 12 + 2714 + 2722 + 1 + 1 + 9 + 9 + 0 + 9 + CCGTCGTGA + CCGTCGTGA + ||||||||| + + + 3 + 14.3694 + 7 + 185.82 + 8 + 14 + 2838 + 2844 + 1 + 1 + 7 + 7 + 0 + 7 + CGTGAAG + CGTGAAG + ||||||| + + + + + 41 + gi|358440111|pdb|4A18|1 + Chain 1, T.Thermophila 60s Ribosomal Subunit In Complex With Initiation Factor 6. This File Contains 26s Rrna And Proteins Of Molecule 1 + 4A18_1 + 3354 + + + 1 + 18.3341 + 9 + 11.9013 + 7 + 15 + 2513 + 2521 + 1 + 1 + 9 + 9 + 0 + 9 + TCGTGAAGA + TCGTGAAGA + ||||||||| + + + 2 + 18.3341 + 9 + 11.9013 + 4 + 12 + 2947 + 2955 + 1 + 1 + 9 + 9 + 0 + 9 + CCGTCGTGA + CCGTCGTGA + ||||||||| + + + 3 + 14.3694 + 7 + 185.82 + 8 + 14 + 3071 + 3077 + 1 + 1 + 7 + 7 + 0 + 7 + CGTGAAG + CGTGAAG + ||||||| + + + + + 42 + gi|358440157|pdb|4A1B|1 + Chain 1, T.Thermophila 60s Ribosomal Subunit In Complex With Initiation Factor 6. This File Contains 26s Rrna And Proteins Of Molecule 3. >gi|359807703|pdb|4A19|1 Chain 1, T.Thermophila 60s Ribosomal Subunit In Complex With Initiation Factor 6. This File Contains 26s Rrna And Proteins Of Molecule 2. + 4A1B_1 + 3354 + + + 1 + 18.3341 + 9 + 11.9013 + 7 + 15 + 2513 + 2521 + 1 + 1 + 9 + 9 + 0 + 9 + TCGTGAAGA + TCGTGAAGA + ||||||||| + + + 2 + 18.3341 + 9 + 11.9013 + 4 + 12 + 2947 + 2955 + 1 + 1 + 9 + 9 + 0 + 9 + CCGTCGTGA + CCGTCGTGA + ||||||||| + + + 3 + 14.3694 + 7 + 185.82 + 8 + 14 + 3071 + 3077 + 1 + 1 + 7 + 7 + 0 + 7 + CGTGAAG + CGTGAAG + ||||||| + + + + + 43 + gi|357380452|pdb|3J0L|8 + Chain 8, Core Of Mammalian 80s Pre-Ribosome In Complex With Trnas Fitted To A 9.8a Cryo-Em Map: Classic Pre State 1 + 3J0L_8 + 20 + + + 1 + 18.3341 + 9 + 11.9013 + 4 + 12 + 3 + 11 + 1 + 1 + 9 + 9 + 0 + 9 + CCGTCGTGA + CCGTCGTGA + ||||||||| + + + + + 44 + gi|357380483|pdb|3J0O|8 + Chain 8, Core Of Mammalian 80s Pre-Ribosome In Complex With Trnas Fitted To A 9a Cryo-Em Map: Classic Pre State 2 + 3J0O_8 + 20 + + + 1 + 18.3341 + 9 + 11.9013 + 4 + 12 + 3 + 11 + 1 + 1 + 9 + 9 + 0 + 9 + CCGTCGTGA + CCGTCGTGA + ||||||||| + + + + + 45 + gi|315113523|pdb|3O58|1 + Chain 1, Yeast 80s Ribosome. This Entry Consists Of The 60s Subunit Of The First 80s In The Asymmetric Unit. >gi|418837761|pdb|4B6B|5 Chain 5, Cryo-Em Structure Of The 60s Ribosomal Subunit In Complex With Arx1 And Rei1 >gi|597959861|pdb|3J64|1 Chain 1, Arx1 Pre-60s Particle. This Entry Contains The Rrna. + 3O58_1 + 3396 + + + 1 + 18.3341 + 9 + 11.9013 + 4 + 12 + 2959 + 2967 + 1 + 1 + 9 + 9 + 0 + 9 + CCGTCGTGA + CCGTCGTGA + ||||||||| + + + 2 + 16.3517 + 8 + 47.0266 + 8 + 15 + 1634 + 1627 + 1 + -1 + 8 + 8 + 0 + 8 + CGTGAAGA + CGTGAAGA + |||||||| + + + 3 + 16.3517 + 8 + 47.0266 + 9 + 16 + 2435 + 2442 + 1 + 1 + 8 + 8 + 0 + 8 + GTGAAGAG + GTGAAGAG + |||||||| + + + 4 + 14.3694 + 7 + 185.82 + 10 + 16 + 1100 + 1106 + 1 + 1 + 7 + 7 + 0 + 7 + TGAAGAG + TGAAGAG + ||||||| + + + 5 + 14.3694 + 7 + 185.82 + 9 + 15 + 2216 + 2222 + 1 + 1 + 7 + 7 + 0 + 7 + GTGAAGA + GTGAAGA + ||||||| + + + + + 46 + gi|315113568|pdb|3O5H|1 + Chain 1, Yeast 80s Ribosome. This Entry Consists Of The 60s Subunit Of The Second 80s In The Asymmetric Unit. >gi|364506130|pdb|3U5D|1 Chain 1, The Structure Of The Eukaryotic Ribosome At 3.0 A Resolution. This Entry Contains Ribosomal Rna And Ions Of The 60s Subunit, Ribosome A >gi|364506168|pdb|3U5H|5 Chain 5, The Structure Of The Eukaryotic Ribosome At 3.0 A Resolution. This Entry Contains Ribosomal Rna And Ions Of The 60s Subunit, Ribosome B + 3O5H_1 + 3396 + + + 1 + 18.3341 + 9 + 11.9013 + 4 + 12 + 2959 + 2967 + 1 + 1 + 9 + 9 + 0 + 9 + CCGTCGTGA + CCGTCGTGA + ||||||||| + + + 2 + 16.3517 + 8 + 47.0266 + 8 + 15 + 1634 + 1627 + 1 + -1 + 8 + 8 + 0 + 8 + CGTGAAGA + CGTGAAGA + |||||||| + + + 3 + 16.3517 + 8 + 47.0266 + 9 + 16 + 2435 + 2442 + 1 + 1 + 8 + 8 + 0 + 8 + GTGAAGAG + GTGAAGAG + |||||||| + + + 4 + 14.3694 + 7 + 185.82 + 10 + 16 + 1100 + 1106 + 1 + 1 + 7 + 7 + 0 + 7 + TGAAGAG + TGAAGAG + ||||||| + + + 5 + 14.3694 + 7 + 185.82 + 9 + 15 + 2216 + 2222 + 1 + 1 + 7 + 7 + 0 + 7 + GTGAAGA + GTGAAGA + ||||||| + + + + + 47 + gi|315113447|pdb|3O2Z|1 + Chain 1, Yeast 80s Ribosome. This Entry Consists Of The 40s Subunit Of The First 80s In The Asymmetric Unit. + 3O2Z_1 + 1800 + + + 1 + 18.3341 + 9 + 11.9013 + 3 + 11 + 1528 + 1536 + 1 + 1 + 9 + 9 + 0 + 9 + TCCGTCGTG + TCCGTCGTG + ||||||||| + + + 2 + 14.3694 + 7 + 185.82 + 4 + 10 + 1006 + 1012 + 1 + 1 + 7 + 7 + 0 + 7 + CCGTCGT + CCGTCGT + ||||||| + + + 3 + 14.3694 + 7 + 185.82 + 10 + 16 + 1569 + 1563 + 1 + -1 + 7 + 7 + 0 + 7 + TGAAGAG + TGAAGAG + ||||||| + + + + + 48 + gi|315113475|pdb|3O30|1 + Chain 1, Yeast 80s Ribosome. This Entry Consists Of The 40s Subunit Of The Second 80s In The Asymmetric Unit. + 3O30_1 + 1800 + + + 1 + 18.3341 + 9 + 11.9013 + 3 + 11 + 1528 + 1536 + 1 + 1 + 9 + 9 + 0 + 9 + TCCGTCGTG + TCCGTCGTG + ||||||||| + + + 2 + 14.3694 + 7 + 185.82 + 4 + 10 + 1006 + 1012 + 1 + 1 + 7 + 7 + 0 + 7 + CCGTCGT + CCGTCGT + ||||||| + + + 3 + 14.3694 + 7 + 185.82 + 10 + 16 + 1569 + 1563 + 1 + -1 + 7 + 7 + 0 + 7 + TGAAGAG + TGAAGAG + ||||||| + + + + + 49 + gi|313103747|pdb|3IZF|A + Chain A, Model Of The Large Subunit Rna Based On A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae Translating 80s Ribosome (With Es27l-In Conformation) + 3IZF_A + 3396 + + + 1 + 18.3341 + 9 + 11.9013 + 4 + 12 + 2959 + 2967 + 1 + 1 + 9 + 9 + 0 + 9 + CCGTCGTGA + CCGTCGTGA + ||||||||| + + + 2 + 16.3517 + 8 + 47.0266 + 8 + 15 + 1634 + 1627 + 1 + -1 + 8 + 8 + 0 + 8 + CGTGAAGA + CGTGAAGA + |||||||| + + + 3 + 16.3517 + 8 + 47.0266 + 9 + 16 + 2435 + 2442 + 1 + 1 + 8 + 8 + 0 + 8 + GTGAAGAG + GTGAAGAG + |||||||| + + + 4 + 14.3694 + 7 + 185.82 + 10 + 16 + 1100 + 1106 + 1 + 1 + 7 + 7 + 0 + 7 + TGAAGAG + TGAAGAG + ||||||| + + + 5 + 14.3694 + 7 + 185.82 + 9 + 15 + 2216 + 2222 + 1 + 1 + 7 + 7 + 0 + 7 + GTGAAGA + GTGAAGA + ||||||| + + + + + 50 + gi|313103744|pdb|3IZE|A + Chain A, Model Of The Small Subunit Rna Based On A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae Translating 80s Ribosome + 3IZE_A + 1800 + + + 1 + 18.3341 + 9 + 11.9013 + 3 + 11 + 1528 + 1536 + 1 + 1 + 9 + 9 + 0 + 9 + TCCGTCGTG + TCCGTCGTG + ||||||||| + + + 2 + 14.3694 + 7 + 185.82 + 4 + 10 + 1006 + 1012 + 1 + 1 + 7 + 7 + 0 + 7 + CCGTCGT + CCGTCGT + ||||||| + + + 3 + 14.3694 + 7 + 185.82 + 10 + 16 + 1569 + 1563 + 1 + -1 + 7 + 7 + 0 + 7 + TGAAGAG + TGAAGAG + ||||||| + + + + + 51 + gi|296278448|pdb|3KO2|I + Chain I, I-Msoi Re-Designed For Altered Dna Cleavage Specificity (-7c) + 3KO2_I + 24 + + + 1 + 18.3341 + 9 + 11.9013 + 4 + 12 + 19 + 11 + 1 + -1 + 9 + 9 + 0 + 9 + CCGTCGTGA + CCGTCGTGA + ||||||||| + + + + + 52 + gi|296278447|pdb|3KO2|H + Chain H, I-Msoi Re-Designed For Altered Dna Cleavage Specificity (-7c) + 3KO2_H + 24 + + + 1 + 18.3341 + 9 + 11.9013 + 4 + 12 + 6 + 14 + 1 + 1 + 9 + 9 + 0 + 9 + CCGTCGTGA + CCGTCGTGA + ||||||||| + + + + + 53 + gi|296278444|pdb|3KO2|D + Chain D, I-Msoi Re-Designed For Altered Dna Cleavage Specificity (-7c) + 3KO2_D + 24 + + + 1 + 18.3341 + 9 + 11.9013 + 4 + 12 + 19 + 11 + 1 + -1 + 9 + 9 + 0 + 9 + CCGTCGTGA + CCGTCGTGA + ||||||||| + + + + + 54 + gi|296278443|pdb|3KO2|C + Chain C, I-Msoi Re-Designed For Altered Dna Cleavage Specificity (-7c) + 3KO2_C + 24 + + + 1 + 18.3341 + 9 + 11.9013 + 4 + 12 + 6 + 14 + 1 + 1 + 9 + 9 + 0 + 9 + CCGTCGTGA + CCGTCGTGA + ||||||||| + + + + + 55 + gi|290790096|pdb|3I56|0 + Chain 0, Co-Crystal Structure Of Triacetyloleandomcyin Bound To The Large Ribosomal Subunit + 3I56_0 + 2923 + + + 1 + 18.3341 + 9 + 11.9013 + 7 + 15 + 305 + 297 + 1 + -1 + 9 + 9 + 0 + 9 + TCGTGAAGA + TCGTGAAGA + ||||||||| + + + 2 + 18.3341 + 9 + 11.9013 + 4 + 12 + 2625 + 2633 + 1 + 1 + 9 + 9 + 0 + 9 + CCGTCGTGA + CCGTCGTGA + ||||||||| + + + 3 + 14.3694 + 7 + 185.82 + 6 + 12 + 2606 + 2612 + 1 + 1 + 7 + 7 + 0 + 7 + GTCGTGA + GTCGTGA + ||||||| + + + + + 56 + gi|281500859|pdb|3JYX|5 + Chain 5, Structure Of The 60s Rrna For Eukaryotic Ribosome Based On Cryo-Em Map Of Thermomyces Lanuginosus Ribosome At 8.9a Resolution + 3JYX_5 + 3170 + + + 1 + 18.3341 + 9 + 11.9013 + 4 + 12 + 2740 + 2748 + 1 + 1 + 9 + 9 + 0 + 9 + CCGTCGTGA + CCGTCGTGA + ||||||||| + + + 2 + 16.3517 + 8 + 47.0266 + 8 + 15 + 1587 + 1580 + 1 + -1 + 8 + 8 + 0 + 8 + CGTGAAGA + CGTGAAGA + |||||||| + + + 3 + 16.3517 + 8 + 47.0266 + 9 + 16 + 2222 + 2229 + 1 + 1 + 8 + 8 + 0 + 8 + GTGAAGAG + GTGAAGAG + |||||||| + + + 4 + 14.3694 + 7 + 185.82 + 6 + 12 + 1344 + 1350 + 1 + 1 + 7 + 7 + 0 + 7 + GTCGTGA + GTCGTGA + ||||||| + + + 5 + 14.3694 + 7 + 185.82 + 9 + 15 + 2003 + 2009 + 1 + 1 + 7 + 7 + 0 + 7 + GTGAAGA + GTGAAGA + ||||||| + + + + + 57 + gi|281500807|pdb|3JYV|A + Chain A, Structure Of The 40s Rrna And Proteins And PE TRNA FOR EUKARYOTIC Ribosome Based On Cryo-Em Map Of Thermomyces Lanuginosus Ribosome At 8.9a Resolution + 3JYV_A + 1761 + + + 1 + 18.3341 + 9 + 11.9013 + 3 + 11 + 1492 + 1500 + 1 + 1 + 9 + 9 + 0 + 9 + TCCGTCGTG + TCCGTCGTG + ||||||||| + + + 2 + 14.3694 + 7 + 185.82 + 4 + 10 + 981 + 987 + 1 + 1 + 7 + 7 + 0 + 7 + CCGTCGT + CCGTCGT + ||||||| + + + 3 + 14.3694 + 7 + 185.82 + 10 + 16 + 1533 + 1527 + 1 + -1 + 7 + 7 + 0 + 7 + TGAAGAG + TGAAGAG + ||||||| + + + + + 58 + gi|259090425|pdb|1S1I|3 + Chain 3, Structure Of The Ribosomal 80s-Eef2-Sordarin Complex From Yeast Obtained By Docking Atomic Models For Rna And Protein Components Into A 11.7 A Cryo-Em Map. This File, 1s1i, Contains 60s Subunit. The 40s Ribosomal Subunit Is In File 1s1h. + 1S1I_3 + 2999 + + + 1 + 18.3341 + 9 + 11.9013 + 4 + 12 + 2710 + 2718 + 1 + 1 + 9 + 9 + 0 + 9 + CCGTCGTGA + CCGTCGTGA + ||||||||| + + + 2 + 14.3694 + 7 + 185.82 + 6 + 12 + 2691 + 2697 + 1 + 1 + 7 + 7 + 0 + 7 + GTCGTGA + GTCGTGA + ||||||| + + + + + 59 + gi|208435493|pdb|2QEX|0 + Chain 0, Negamycin Binds To The Wall Of The Nascent Chain Exit Tunnel Of The 50s Ribosomal Subunit + 2QEX_0 + 2772 + + + 1 + 18.3341 + 9 + 11.9013 + 4 + 12 + 2476 + 2484 + 1 + 1 + 9 + 9 + 0 + 9 + CCGTCGTGA + CCGTCGTGA + ||||||||| + + + 2 + 14.3694 + 7 + 185.82 + 6 + 12 + 2457 + 2463 + 1 + 1 + 7 + 7 + 0 + 7 + GTCGTGA + GTCGTGA + ||||||| + + + + + 60 + gi|194368703|pdb|3CPW|0 + Chain 0, The Structure Of The Antibiotic Linezolid Bound To The Large Ribosomal Subunit Of Haloarcula Marismortui + 3CPW_0 + 2922 + + + 1 + 18.3341 + 9 + 11.9013 + 4 + 12 + 2624 + 2632 + 1 + 1 + 9 + 9 + 0 + 9 + CCGTCGTGA + CCGTCGTGA + ||||||||| + + + 2 + 14.3694 + 7 + 185.82 + 6 + 12 + 2605 + 2611 + 1 + 1 + 7 + 7 + 0 + 7 + GTCGTGA + GTCGTGA + ||||||| + + + + + 61 + gi|188596372|pdb|3CCV|0 + Chain 0, Structure Of Anisomycin Resistant 50s Ribosomal Subunit: 23s Rrna Mutation G2616a >gi|188596403|pdb|3CD6|0 Chain 0, Co-cystal Of Large Ribosomal Subunit Mutant G2616a With Cc-puromycin + 3CCV_0 + 2923 + + + 1 + 18.3341 + 9 + 11.9013 + 7 + 15 + 305 + 297 + 1 + -1 + 9 + 9 + 0 + 9 + TCGTGAAGA + TCGTGAAGA + ||||||||| + + + 2 + 18.3341 + 9 + 11.9013 + 4 + 12 + 2625 + 2633 + 1 + 1 + 9 + 9 + 0 + 9 + CCGTCGTGA + CCGTCGTGA + ||||||||| + + + 3 + 14.3694 + 7 + 185.82 + 6 + 12 + 2606 + 2612 + 1 + 1 + 7 + 7 + 0 + 7 + GTCGTGA + GTCGTGA + ||||||| + + + + + 62 + gi|188596341|pdb|3CCU|0 + Chain 0, Structure Of Anisomycin Resistant 50s Ribosomal Subunit: 23s Rrna Mutation G2482c + 3CCU_0 + 2923 + + + 1 + 18.3341 + 9 + 11.9013 + 7 + 15 + 305 + 297 + 1 + -1 + 9 + 9 + 0 + 9 + TCGTGAAGA + TCGTGAAGA + ||||||||| + + + 2 + 18.3341 + 9 + 11.9013 + 4 + 12 + 2625 + 2633 + 1 + 1 + 9 + 9 + 0 + 9 + CCGTCGTGA + CCGTCGTGA + ||||||||| + + + 3 + 14.3694 + 7 + 185.82 + 6 + 12 + 2606 + 2612 + 1 + 1 + 7 + 7 + 0 + 7 + GTCGTGA + GTCGTGA + ||||||| + + + + + 63 + gi|188596310|pdb|3CCS|0 + Chain 0, Structure Of Anisomycin Resistant 50s Ribosomal Subunit: 23s Rrna Mutation G2482a + 3CCS_0 + 2923 + + + 1 + 18.3341 + 9 + 11.9013 + 7 + 15 + 305 + 297 + 1 + -1 + 9 + 9 + 0 + 9 + TCGTGAAGA + TCGTGAAGA + ||||||||| + + + 2 + 18.3341 + 9 + 11.9013 + 4 + 12 + 2625 + 2633 + 1 + 1 + 9 + 9 + 0 + 9 + CCGTCGTGA + CCGTCGTGA + ||||||||| + + + 3 + 14.3694 + 7 + 185.82 + 6 + 12 + 2606 + 2612 + 1 + 1 + 7 + 7 + 0 + 7 + GTCGTGA + GTCGTGA + ||||||| + + + + + 64 + gi|188596279|pdb|3CCR|0 + Chain 0, Structure Of Anisomycin Resistant 50s Ribosomal Subunit: 23s Rrna Mutation A2488c. Density For Anisomycin Is Visible But Not Included In The Model. + 3CCR_0 + 2923 + + + 1 + 18.3341 + 9 + 11.9013 + 7 + 15 + 305 + 297 + 1 + -1 + 9 + 9 + 0 + 9 + TCGTGAAGA + TCGTGAAGA + ||||||||| + + + 2 + 18.3341 + 9 + 11.9013 + 4 + 12 + 2625 + 2633 + 1 + 1 + 9 + 9 + 0 + 9 + CCGTCGTGA + CCGTCGTGA + ||||||||| + + + 3 + 14.3694 + 7 + 185.82 + 6 + 12 + 2606 + 2612 + 1 + 1 + 7 + 7 + 0 + 7 + GTCGTGA + GTCGTGA + ||||||| + + + + + 65 + gi|188596248|pdb|3CCQ|0 + Chain 0, Structure Of Anisomycin Resistant 50s Ribosomal Subunit: 23s Rrna Mutation A2488u + 3CCQ_0 + 2923 + + + 1 + 18.3341 + 9 + 11.9013 + 7 + 15 + 305 + 297 + 1 + -1 + 9 + 9 + 0 + 9 + TCGTGAAGA + TCGTGAAGA + ||||||||| + + + 2 + 18.3341 + 9 + 11.9013 + 4 + 12 + 2625 + 2633 + 1 + 1 + 9 + 9 + 0 + 9 + CCGTCGTGA + CCGTCGTGA + ||||||||| + + + 3 + 14.3694 + 7 + 185.82 + 6 + 12 + 2606 + 2612 + 1 + 1 + 7 + 7 + 0 + 7 + GTCGTGA + GTCGTGA + ||||||| + + + + + 66 + gi|188596217|pdb|3CCM|0 + Chain 0, Structure Of Anisomycin Resistant 50s Ribosomal Subunit: 23s Rrna Mutation G2611u + 3CCM_0 + 2923 + + + 1 + 18.3341 + 9 + 11.9013 + 7 + 15 + 305 + 297 + 1 + -1 + 9 + 9 + 0 + 9 + TCGTGAAGA + TCGTGAAGA + ||||||||| + + + 2 + 18.3341 + 9 + 11.9013 + 4 + 12 + 2625 + 2633 + 1 + 1 + 9 + 9 + 0 + 9 + CCGTCGTGA + CCGTCGTGA + ||||||||| + + + + + 67 + gi|188596186|pdb|3CCL|0 + Chain 0, Structure Of Anisomycin Resistant 50s Ribosomal Subunit: 23s Rrna Mutation U2535c. Density For Anisomycin Is Visible But Not Included In Model. + 3CCL_0 + 2923 + + + 1 + 18.3341 + 9 + 11.9013 + 7 + 15 + 305 + 297 + 1 + -1 + 9 + 9 + 0 + 9 + TCGTGAAGA + TCGTGAAGA + ||||||||| + + + 2 + 18.3341 + 9 + 11.9013 + 4 + 12 + 2625 + 2633 + 1 + 1 + 9 + 9 + 0 + 9 + CCGTCGTGA + CCGTCGTGA + ||||||||| + + + 3 + 14.3694 + 7 + 185.82 + 6 + 12 + 2606 + 2612 + 1 + 1 + 7 + 7 + 0 + 7 + GTCGTGA + GTCGTGA + ||||||| + + + + + 68 + gi|188596155|pdb|3CCJ|0 + Chain 0, Structure Of Anisomycin Resistant 50s Ribosomal Subunit: 23s Rrna Mutation C2534u + 3CCJ_0 + 2923 + + + 1 + 18.3341 + 9 + 11.9013 + 7 + 15 + 305 + 297 + 1 + -1 + 9 + 9 + 0 + 9 + TCGTGAAGA + TCGTGAAGA + ||||||||| + + + 2 + 18.3341 + 9 + 11.9013 + 4 + 12 + 2625 + 2633 + 1 + 1 + 9 + 9 + 0 + 9 + CCGTCGTGA + CCGTCGTGA + ||||||||| + + + 3 + 14.3694 + 7 + 185.82 + 6 + 12 + 2606 + 2612 + 1 + 1 + 7 + 7 + 0 + 7 + GTCGTGA + GTCGTGA + ||||||| + + + + + 69 + gi|188596124|pdb|3CCE|0 + Chain 0, Structure Of Anisomycin Resistant 50s Ribosomal Subunit: 23s Rrna Mutation U2535a + 3CCE_0 + 2923 + + + 1 + 18.3341 + 9 + 11.9013 + 7 + 15 + 305 + 297 + 1 + -1 + 9 + 9 + 0 + 9 + TCGTGAAGA + TCGTGAAGA + ||||||||| + + + 2 + 18.3341 + 9 + 11.9013 + 4 + 12 + 2625 + 2633 + 1 + 1 + 9 + 9 + 0 + 9 + CCGTCGTGA + CCGTCGTGA + ||||||||| + + + 3 + 14.3694 + 7 + 185.82 + 6 + 12 + 2606 + 2612 + 1 + 1 + 7 + 7 + 0 + 7 + GTCGTGA + GTCGTGA + ||||||| + + + + + 70 + gi|188596093|pdb|3CC7|0 + Chain 0, Structure Of Anisomycin Resistant 50s Ribosomal Subunit: 23s Rrna Mutation C2487u + 3CC7_0 + 2923 + + + 1 + 18.3341 + 9 + 11.9013 + 7 + 15 + 305 + 297 + 1 + -1 + 9 + 9 + 0 + 9 + TCGTGAAGA + TCGTGAAGA + ||||||||| + + + 2 + 18.3341 + 9 + 11.9013 + 4 + 12 + 2625 + 2633 + 1 + 1 + 9 + 9 + 0 + 9 + CCGTCGTGA + CCGTCGTGA + ||||||||| + + + 3 + 14.3694 + 7 + 185.82 + 6 + 12 + 2606 + 2612 + 1 + 1 + 7 + 7 + 0 + 7 + GTCGTGA + GTCGTGA + ||||||| + + + + + 71 + gi|188596031|pdb|3CC2|0 + Chain 0, The Refined Crystal Structure Of The Haloarcula Marismortui Large Ribosomal Subunit At 2.4 Angstrom Resolution With Rrna Sequence For The 23s Rrna And Genome-Derived Sequences For R-Proteins >gi|188596062|pdb|3CC4|0 Chain 0, Co-Crystal Structure Of Anisomycin Bound To The 50s Ribosomal Subunit >gi|206581937|pdb|3CMA|0 Chain 0, The Structure Of Cca And Cca-Phe-Cap-Bio Bound To The Large Ribosomal Subunit Of Haloarcula Marismortui >gi|206581970|pdb|3CME|0 Chain 0, The Structure Of Ca And Cca-Phe-Cap-Bio Bound To The Large Ribosomal Subunit Of Haloarcula Marismortui >gi|228312141|pdb|3G4S|0 Chain 0, Co-Crystal Structure Of Tiamulin Bound To The Large Ribosomal Subunit >gi|228312197|pdb|3G6E|0 Chain 0, Co-Crystal Structure Of Homoharringtonine Bound To The Large Ribosomal Subunit >gi|228312233|pdb|3G71|0 Chain 0, Co-crystal Structure Of Bruceantin Bound To The Large Ribosomal Subunit >gi|290790035|pdb|3I55|0 Chain 0, Co-Crystal Structure Of Mycalamide A Bound To The Large Ribosomal Subunit + 3CC2_0 + 2923 + + + 1 + 18.3341 + 9 + 11.9013 + 7 + 15 + 305 + 297 + 1 + -1 + 9 + 9 + 0 + 9 + TCGTGAAGA + TCGTGAAGA + ||||||||| + + + 2 + 18.3341 + 9 + 11.9013 + 4 + 12 + 2625 + 2633 + 1 + 1 + 9 + 9 + 0 + 9 + CCGTCGTGA + CCGTCGTGA + ||||||||| + + + 3 + 14.3694 + 7 + 185.82 + 6 + 12 + 2606 + 2612 + 1 + 1 + 7 + 7 + 0 + 7 + GTCGTGA + GTCGTGA + ||||||| + + + + + 72 + gi|187609272|pdb|2ZKR|0 + Chain 0, Structure Of A Mammalian Ribosomal 60s Subunit Within An 80s Complex Obtained By Docking Homology Models Of The Rna And Proteins Into An 8.7 A Cryo-Em Map + 2ZKR_0 + 2903 + + + 1 + 18.3341 + 9 + 11.9013 + 4 + 12 + 2623 + 2631 + 1 + 1 + 9 + 9 + 0 + 9 + CCGTCGTGA + CCGTCGTGA + ||||||||| + + + 2 + 16.3517 + 8 + 47.0266 + 9 + 16 + 2111 + 2118 + 1 + 1 + 8 + 8 + 0 + 8 + GTGAAGAG + GTGAAGAG + |||||||| + + + 3 + 14.3694 + 7 + 185.82 + 10 + 16 + 353 + 359 + 1 + 1 + 7 + 7 + 0 + 7 + TGAAGAG + TGAAGAG + ||||||| + + + 4 + 14.3694 + 7 + 185.82 + 9 + 15 + 1892 + 1898 + 1 + 1 + 7 + 7 + 0 + 7 + GTGAAGA + GTGAAGA + ||||||| + + + + + 73 + gi|171848835|pdb|2QA4|0 + Chain 0, A More Complete Structure Of The The L7L12 STALK OF THE Haloarcula Marismortui 50s Large Ribosomal Subunit + 2QA4_0 + 2922 + + + 1 + 18.3341 + 9 + 11.9013 + 4 + 12 + 2624 + 2632 + 1 + 1 + 9 + 9 + 0 + 9 + CCGTCGTGA + CCGTCGTGA + ||||||||| + + + 2 + 14.3694 + 7 + 185.82 + 6 + 12 + 2605 + 2611 + 1 + 1 + 7 + 7 + 0 + 7 + GTCGTGA + GTCGTGA + ||||||| + + + + + 74 + gi|99032306|pdb|2FTC|R + Chain R, Structural Model For The Large Subunit Of The Mammalian Mitochondrial Ribosome + 2FTC_R + 1568 + + + 1 + 18.3341 + 9 + 11.9013 + 8 + 16 + 1032 + 1040 + 1 + 1 + 9 + 9 + 0 + 9 + CGTGAAGAG + CGTGAAGAG + ||||||||| + + + + + 75 + gi|50513468|pdb|1S72|0 + Chain 0, Refined Crystal Structure Of The Haloarcula Marismortui Large Ribosomal Subunit At 2.4 Angstrom Resolution >gi|83753123|pdb|1VQ4|0 Chain 0, The Structure Of The Transition State Analogue "daa" Bound To The Large Ribosomal Subunit Of Haloarcula Marismortui >gi|83753155|pdb|1VQ5|0 Chain 0, The Structure Of The Transition State Analogue "raa" Bound To The Large Ribosomal Subunit Of Haloarcula Marismortui >gi|83753187|pdb|1VQ6|0 Chain 0, The Structure Of C-Hpmn And Cca-Phe-Cap-Bio Bound To The Large Ribosomal Subunit Of Haloarcula Marismortui >gi|83753219|pdb|1VQ7|0 Chain 0, The Structure Of The Transition State Analogue "dca" Bound To The Large Ribosomal Subunit Of Haloarcula Marismortui >gi|83753251|pdb|1VQ8|0 Chain 0, The Structure Of Ccda-Phe-Cap-Bio And The Antibiotic Sparsomycin Bound To The Large Ribosomal Subunit Of Haloarcula Marismortui >gi|83753282|pdb|1VQ9|0 Chain 0, The Structure Of Cca-Phe-Cap-Bio And The Antibiotic Sparsomycin Bound To The Large Ribosomal Subunit Of Haloarcula Marismortui >gi|83753314|pdb|1VQK|0 Chain 0, The Structure Of Ccda-Phe-Cap-Bio Bound To The A Site Of The Ribosomal Subunit Of Haloarcula Marismortui >gi|83753345|pdb|1VQL|0 Chain 0, The Structure Of The Transition State Analogue "dcsn" Bound To The Large Ribosomal Subunit Of Haloarcula Marismortui >gi|83753376|pdb|1VQM|0 Chain 0, The Structure Of The Transition State Analogue "dan" Bound To The Large Ribosomal Subunit Of Haloarcula Marismortui >gi|83753407|pdb|1VQN|0 Chain 0, The Structure Of Cc-hpmn And Cca-phe-cap-bio Bound To The Large Ribosomal Subunit Of Haloarcula Marismortui >gi|83753439|pdb|1VQO|0 Chain 0, The Structure Of Ccpmn Bound To The Large Ribosomal Subunit Haloarcula Marismortui >gi|83753470|pdb|1VQP|0 Chain 0, The Structure Of The Transition State Analogue "rap" Bound To The Large Ribosomal Subunit Of Haloarcula Marismortui >gi|145580171|pdb|2OTJ|0 Chain 0, 13-Deoxytedanolide Bound To The Large Subunit Of Haloarcula Marismortui >gi|145580202|pdb|2OTL|0 Chain 0, Girodazole Bound To The Large Subunit Of Haloarcula Marismortui + 1S72_0 + 2922 + + + 1 + 18.3341 + 9 + 11.9013 + 4 + 12 + 2624 + 2632 + 1 + 1 + 9 + 9 + 0 + 9 + CCGTCGTGA + CCGTCGTGA + ||||||||| + + + 2 + 14.3694 + 7 + 185.82 + 6 + 12 + 2605 + 2611 + 1 + 1 + 7 + 7 + 0 + 7 + GTCGTGA + GTCGTGA + ||||||| + + + + + 76 + gi|66360881|pdb|1YIT|0 + Chain 0, Crystal Structure Of Virginiamycin M And S Bound To The 50s Ribosomal Subunit Of Haloarcula Marismortui >gi|66360914|pdb|1YJ9|0 Chain 0, Crystal Structure Of The Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui Containing A Three Residue Deletion In L22 + 1YIT_0 + 2922 + + + 1 + 18.3341 + 9 + 11.9013 + 7 + 15 + 305 + 297 + 1 + -1 + 9 + 9 + 0 + 9 + TCGTGAAGA + TCGTGAAGA + ||||||||| + + + 2 + 18.3341 + 9 + 11.9013 + 4 + 12 + 2625 + 2633 + 1 + 1 + 9 + 9 + 0 + 9 + CCGTCGTGA + CCGTCGTGA + ||||||||| + + + 3 + 14.3694 + 7 + 185.82 + 6 + 12 + 2606 + 2612 + 1 + 1 + 7 + 7 + 0 + 7 + GTCGTGA + GTCGTGA + ||||||| + + + + + 77 + gi|66360782|pdb|1YHQ|0 + Chain 0, Crystal Structure Of Azithromycin Bound To The G2099a Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui >gi|66360815|pdb|1YI2|0 Chain 0, Crystal Structure Of Erythromycin Bound To The G2099a Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui >gi|66360848|pdb|1YIJ|0 Chain 0, Crystal Structure Of Telithromycin Bound To The G2099a Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui >gi|66360947|pdb|1YJN|0 Chain 0, Crystal Structure Of Clindamycin Bound To The G2099a Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui + 1YHQ_0 + 2922 + + + 1 + 18.3341 + 9 + 11.9013 + 7 + 15 + 305 + 297 + 1 + -1 + 9 + 9 + 0 + 9 + TCGTGAAGA + TCGTGAAGA + ||||||||| + + + 2 + 18.3341 + 9 + 11.9013 + 4 + 12 + 2625 + 2633 + 1 + 1 + 9 + 9 + 0 + 9 + CCGTCGTGA + CCGTCGTGA + ||||||||| + + + 3 + 14.3694 + 7 + 185.82 + 6 + 12 + 2606 + 2612 + 1 + 1 + 7 + 7 + 0 + 7 + GTCGTGA + GTCGTGA + ||||||| + + + + + 78 + gi|66360980|pdb|1YJW|0 + Chain 0, Crystal Structure Of Quinupristin Bound To The G2099a Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui + 1YJW_0 + 2922 + + + 1 + 18.3341 + 9 + 11.9013 + 7 + 15 + 305 + 297 + 1 + -1 + 9 + 9 + 0 + 9 + TCGTGAAGA + TCGTGAAGA + ||||||||| + + + 2 + 18.3341 + 9 + 11.9013 + 4 + 12 + 2625 + 2633 + 1 + 1 + 9 + 9 + 0 + 9 + CCGTCGTGA + CCGTCGTGA + ||||||||| + + + 3 + 14.3694 + 7 + 185.82 + 6 + 12 + 2606 + 2612 + 1 + 1 + 7 + 7 + 0 + 7 + GTCGTGA + GTCGTGA + ||||||| + + + + + 79 + gi|37928006|pdb|1Q86|A + Chain A, Crystal Structure Of Cca-Phe-Cap-Biotin Bound Simultaneously At Half Occupancy To Both The A-Site And P- Site Of The The 50s Ribosomal Subunit. + 1Q86_A + 2922 + + + 1 + 18.3341 + 9 + 11.9013 + 4 + 12 + 2624 + 2632 + 1 + 1 + 9 + 9 + 0 + 9 + CCGTCGTGA + CCGTCGTGA + ||||||||| + + + 2 + 14.3694 + 7 + 185.82 + 6 + 12 + 2605 + 2611 + 1 + 1 + 7 + 7 + 0 + 7 + GTCGTGA + GTCGTGA + ||||||| + + + + + 80 + gi|15825941|pdb|1JJ2|0 + Chain 0, Fully Refined Crystal Structure Of The Haloarcula Marismortui Large Ribosomal Subunit At 2.4 Angstrom Resolution >gi|20150986|pdb|1KQS|0 Chain 0, The Haloarcula Marismortui 50s Complexed With A Pretranslocational Intermediate In Protein Synthesis >gi|22219324|pdb|1M1K|A Chain A, Co-Crystal Structure Of Azithromycin Bound To The 50s Ribosomal Subunit Of Haloarcula Marismortui >gi|24159019|pdb|1M90|A Chain A, Co-Crystal Structure Of Cca-Phe-Caproic Acid-Biotin And Sparsomycin Bound To The 50s Ribosomal Subunit >gi|34811116|pdb|1K73|A Chain A, Co-Crystal Structure Of Anisomycin Bound To The 50s Ribosomal Subunit >gi|34811185|pdb|1N8R|A Chain A, Structure Of Large Ribosomal Subunit In Complex With Virginiamycin M >gi|34811215|pdb|1NJI|A Chain A, Structure Of Chloramphenicol Bound To The 50s Ribosomal Subunit >gi|37927899|pdb|1Q7Y|A Chain A, Crystal Structure Of Ccdap-puromycin Bound At The Peptidyl Transferase Center Of The 50s Ribosomal Subunit >gi|37927934|pdb|1Q81|A Chain A, Crystal Structure Of Minihelix With 3' Puromycin Bound To A- Site Of The 50s Ribosomal Subunit. >gi|37927970|pdb|1Q82|A Chain A, Crystal Structure Of Cc-Puromycin Bound To The A-Site Of The 50s Ribosomal Subunit >gi|39654670|pdb|1QVF|0 Chain 0, Structure Of A Deacylated Trna Minihelix Bound To The E Site Of The Large Ribosomal Subunit Of Haloarcula Marismortui >gi|39654701|pdb|1QVG|0 Chain 0, Structure Of Cca Oligonucleotide Bound To The Trna Binding Sites Of The Large Ribosomal Subunit Of Haloarcula Marismortui >gi|157878615|pdb|1K8A|A Chain A, Co-Crystal Structure Of Carbomycin A Bound To The 50s Ribosomal Subunit Of Haloarcula Marismortui >gi|157878625|pdb|1K9M|A Chain A, Co-Crystal Structure Of Tylosin Bound To The 50s Ribosomal Subunit Of Haloarcula Marismortui >gi|157878639|pdb|1KD1|A Chain A, Co-crystal Structure Of Spiramycin Bound To The 50s Ribosomal Subunit Of Haloarcula Marismortui >gi|157880605|pdb|1W2B|0 Chain 0, Trigger Factor Ribosome Binding Domain In Complex With 50s >gi|228311909|pdb|3CXC|0 Chain 0, The Structure Of An Enhanced Oxazolidinone Inhibitor Bound To The 50s Ribosomal Subunit Of H. Marismortui + 1JJ2_0 + 2922 + + + 1 + 18.3341 + 9 + 11.9013 + 4 + 12 + 2624 + 2632 + 1 + 1 + 9 + 9 + 0 + 9 + CCGTCGTGA + CCGTCGTGA + ||||||||| + + + 2 + 14.3694 + 7 + 185.82 + 6 + 12 + 2605 + 2611 + 1 + 1 + 7 + 7 + 0 + 7 + GTCGTGA + GTCGTGA + ||||||| + + + + + 81 + gi|34811146|pdb|1KC8|A + Chain A, Co-Crystal Structure Of Blasticidin S Bound To The 50s Ribosomal Subunit + 1KC8_A + 2922 + + + 1 + 18.3341 + 9 + 11.9013 + 4 + 12 + 2624 + 2632 + 1 + 1 + 9 + 9 + 0 + 9 + CCGTCGTGA + CCGTCGTGA + ||||||||| + + + 2 + 14.3694 + 7 + 185.82 + 6 + 12 + 2605 + 2611 + 1 + 1 + 7 + 7 + 0 + 7 + GTCGTGA + GTCGTGA + ||||||| + + + + + 82 + gi|10120918|pdb|1FFK|0 + Chain 0, Crystal Structure Of The Large Ribosomal Subunit From Haloarcula Marismortui At 2.4 Angstrom Resolution + 1FFK_0 + 2922 + + + 1 + 18.3341 + 9 + 11.9013 + 4 + 12 + 2624 + 2632 + 1 + 1 + 9 + 9 + 0 + 9 + CCGTCGTGA + CCGTCGTGA + ||||||||| + + + 2 + 14.3694 + 7 + 185.82 + 6 + 12 + 2605 + 2611 + 1 + 1 + 7 + 7 + 0 + 7 + GTCGTGA + GTCGTGA + ||||||| + + + + + 83 + gi|10120728|pdb|1FG0|A + Chain A, Large Ribosomal Subunit Complexed With A 13 Bp Minihelix- Puromycin Compound + 1FG0_A + 602 + + + 1 + 18.3341 + 9 + 11.9013 + 4 + 12 + 563 + 571 + 1 + 1 + 9 + 9 + 0 + 9 + CCGTCGTGA + CCGTCGTGA + ||||||||| + + + 2 + 14.3694 + 7 + 185.82 + 6 + 12 + 544 + 550 + 1 + 1 + 7 + 7 + 0 + 7 + GTCGTGA + GTCGTGA + ||||||| + + + + + 84 + gi|10120727|pdb|1FFZ|A + Chain A, Large Ribosomal Subunit Complexed With R(Cc)-Da-Puromycin + 1FFZ_A + 602 + + + 1 + 18.3341 + 9 + 11.9013 + 4 + 12 + 563 + 571 + 1 + 1 + 9 + 9 + 0 + 9 + CCGTCGTGA + CCGTCGTGA + ||||||||| + + + 2 + 14.3694 + 7 + 185.82 + 6 + 12 + 544 + 550 + 1 + 1 + 7 + 7 + 0 + 7 + GTCGTGA + GTCGTGA + ||||||| + + + + + 85 + gi|558705015|pdb|4LGT|F + Chain F, Crystal Structure Of The Catalytic Domain Of Rlub In Complex With A 21-nucleotide Rna Substrate + 4LGT_F + 21 + + + 1 + 16.3517 + 8 + 47.0266 + 5 + 12 + 5 + 12 + 1 + 1 + 8 + 8 + 0 + 8 + CGTCGTGA + CGTCGTGA + |||||||| + + + + + 86 + gi|558705013|pdb|4LGT|E + Chain E, Crystal Structure Of The Catalytic Domain Of Rlub In Complex With A 21-nucleotide Rna Substrate + 4LGT_E + 21 + + + 1 + 16.3517 + 8 + 47.0266 + 5 + 12 + 5 + 12 + 1 + 1 + 8 + 8 + 0 + 8 + CGTCGTGA + CGTCGTGA + |||||||| + + + + + 87 + gi|529280935|pdb|4BTD|A + Chain A, Thermus Thermophilus Ribosome + 4BTD_A + 2915 + + + 1 + 16.3517 + 8 + 47.0266 + 8 + 15 + 2048 + 2055 + 1 + 1 + 8 + 8 + 0 + 8 + CGTGAAGA + CGTGAAGA + |||||||| + + + 2 + 16.3517 + 8 + 47.0266 + 5 + 12 + 2603 + 2610 + 1 + 1 + 8 + 8 + 0 + 8 + CGTCGTGA + CGTCGTGA + |||||||| + + + + + 88 + gi|528082310|pdb|4L6J|A + Chain A, Crystal Structure Of Blasticidin S Bound To Thermus Thermophilus 70s Ribosome. This File Contains The 50s Subunit And Blasticidin S Molecule From The First 70s Ribosome. >gi|528082364|pdb|4L6L|A Chain A, Crystal Structure Of Blasticidin S Bound To Thermus Thermophilus 70s Ribosome. This File Contains The 50s Subunit And Blasticidin S Molecule From The Second 70s Ribosome + 4L6J_A + 2879 + + + 1 + 16.3517 + 8 + 47.0266 + 8 + 15 + 2021 + 2028 + 1 + 1 + 8 + 8 + 0 + 8 + CGTGAAGA + CGTGAAGA + |||||||| + + + 2 + 16.3517 + 8 + 47.0266 + 5 + 12 + 2576 + 2583 + 1 + 1 + 8 + 8 + 0 + 8 + CGTCGTGA + CGTCGTGA + |||||||| + + + + + 89 + gi|520729408|pdb|4KFI|A + Chain A, Crystal Structure Of The 70s Ribosome Bound With The Q253p Mutant Of Release Factor Rf2. 50s Of The A Subunit >gi|520729463|pdb|4KFL|A Chain A, Crystal Structure Of The 70s Ribosome Bound With The Q253p Mutant Of Release Factor Rf2. 50s Of The B Subunit + 4KFI_A + 2879 + + + 1 + 16.3517 + 8 + 47.0266 + 8 + 15 + 2021 + 2028 + 1 + 1 + 8 + 8 + 0 + 8 + CGTGAAGA + CGTGAAGA + |||||||| + + + 2 + 16.3517 + 8 + 47.0266 + 5 + 12 + 2576 + 2583 + 1 + 1 + 8 + 8 + 0 + 8 + CGTCGTGA + CGTCGTGA + |||||||| + + + + + 90 + gi|520728860|pdb|4K0Q|A + Chain A, Crystal Structure Of Thermus Thermophilus 70s Containing Trnas And Mrna Stop Codon With Pseudouridine + 4K0Q_A + 2915 + + + 1 + 16.3517 + 8 + 47.0266 + 8 + 15 + 2048 + 2055 + 1 + 1 + 8 + 8 + 0 + 8 + CGTGAAGA + CGTGAAGA + |||||||| + + + 2 + 16.3517 + 8 + 47.0266 + 5 + 12 + 2603 + 2610 + 1 + 1 + 8 + 8 + 0 + 8 + CGTCGTGA + CGTCGTGA + |||||||| + + + + + 91 + gi|520728802|pdb|4K0M|A + Chain A, Crystal Structure Of Thermus Thermophilus 70s Containing Trnas And Mrna Stop Codon With Pseudouridine + 4K0M_A + 2915 + + + 1 + 16.3517 + 8 + 47.0266 + 8 + 15 + 2048 + 2055 + 1 + 1 + 8 + 8 + 0 + 8 + CGTGAAGA + CGTGAAGA + |||||||| + + + 2 + 16.3517 + 8 + 47.0266 + 5 + 12 + 2603 + 2610 + 1 + 1 + 8 + 8 + 0 + 8 + CGTCGTGA + CGTCGTGA + |||||||| + + + + + 92 + gi|512125286|pdb|3J3V|A + Chain A, Atomic Model Of The Immature 50s Subunit From Bacillus Subtilis (state I-a) + 3J3V_A + 2927 + + + 1 + 16.3517 + 8 + 47.0266 + 5 + 12 + 2620 + 2627 + 1 + 1 + 8 + 8 + 0 + 8 + CGTCGTGA + CGTCGTGA + |||||||| + + + 2 + 14.3694 + 7 + 185.82 + 10 + 16 + 340 + 346 + 1 + 1 + 7 + 7 + 0 + 7 + TGAAGAG + TGAAGAG + ||||||| + + + 3 + 14.3694 + 7 + 185.82 + 3 + 9 + 440 + 446 + 1 + 1 + 7 + 7 + 0 + 7 + TCCGTCG + TCCGTCG + ||||||| + + + 4 + 14.3694 + 7 + 185.82 + 9 + 15 + 2056 + 2062 + 1 + 1 + 7 + 7 + 0 + 7 + GTGAAGA + GTGAAGA + ||||||| + + + 5 + 14.3694 + 7 + 185.82 + 3 + 9 + 2644 + 2650 + 1 + 1 + 7 + 7 + 0 + 7 + TCCGTCG + TCCGTCG + ||||||| + + + + + 93 + gi|512125306|pdb|3J3W|A + Chain A, Atomic Model Of The Immature 50s Subunit From Bacillus Subtilis (state Ii-a) + 3J3W_A + 2927 + + + 1 + 16.3517 + 8 + 47.0266 + 5 + 12 + 2620 + 2627 + 1 + 1 + 8 + 8 + 0 + 8 + CGTCGTGA + CGTCGTGA + |||||||| + + + 2 + 14.3694 + 7 + 185.82 + 10 + 16 + 340 + 346 + 1 + 1 + 7 + 7 + 0 + 7 + TGAAGAG + TGAAGAG + ||||||| + + + 3 + 14.3694 + 7 + 185.82 + 3 + 9 + 440 + 446 + 1 + 1 + 7 + 7 + 0 + 7 + TCCGTCG + TCCGTCG + ||||||| + + + 4 + 14.3694 + 7 + 185.82 + 9 + 15 + 2056 + 2062 + 1 + 1 + 7 + 7 + 0 + 7 + GTGAAGA + GTGAAGA + ||||||| + + + 5 + 14.3694 + 7 + 185.82 + 3 + 9 + 2644 + 2650 + 1 + 1 + 7 + 7 + 0 + 7 + TCCGTCG + TCCGTCG + ||||||| + + + + + 94 + gi|482676744|pdb|3V6X|A + Chain A, Crystal Structure Of The Bacterial Ribosome Ram Mutation G347u. This Entry Contains The 50s Ribosomal Subunit Of The Second 70s Molecule In The Asymmetric Unit + 3V6X_A + 2916 + + + 1 + 16.3517 + 8 + 47.0266 + 8 + 15 + 2048 + 2055 + 1 + 1 + 8 + 8 + 0 + 8 + CGTGAAGA + CGTGAAGA + |||||||| + + + 2 + 16.3517 + 8 + 47.0266 + 5 + 12 + 2603 + 2610 + 1 + 1 + 8 + 8 + 0 + 8 + CGTCGTGA + CGTCGTGA + |||||||| + + + + + 95 + gi|482676712|pdb|3V6W|A + Chain A, Crystal Structure Of The Bacterial Ribosome Ram Mutation G347u. This Entry Contains The 50s Ribosomal Subunit Of The First 70s Molecule In The Asymmetric Unit + 3V6W_A + 2916 + + + 1 + 16.3517 + 8 + 47.0266 + 8 + 15 + 2048 + 2055 + 1 + 1 + 8 + 8 + 0 + 8 + CGTGAAGA + CGTGAAGA + |||||||| + + + 2 + 16.3517 + 8 + 47.0266 + 5 + 12 + 2603 + 2610 + 1 + 1 + 8 + 8 + 0 + 8 + CGTCGTGA + CGTCGTGA + |||||||| + + + + + 96 + gi|428697829|pdb|2YMI|DD + Chain d, The Cryo-Em Structure Of A 3d Dna-Origami Object + 2YMI_DD + 56 + + + 1 + 16.3517 + 8 + 47.0266 + 5 + 12 + 52 + 45 + 1 + -1 + 8 + 8 + 0 + 8 + CGTCGTGA + CGTCGTGA + |||||||| + + + + + 97 + gi|428697789|pdb|2YMF|A + Chain A, The Cryo-Em Structure Of A 3d Dna-Origami Object + 2YMF_A + 4896 + + + 1 + 16.3517 + 8 + 47.0266 + 5 + 12 + 575 + 582 + 1 + 1 + 8 + 8 + 0 + 8 + CGTCGTGA + CGTCGTGA + |||||||| + + + 2 + 14.3694 + 7 + 185.82 + 4 + 10 + 561 + 567 + 1 + 1 + 7 + 7 + 0 + 7 + CCGTCGT + CCGTCGT + ||||||| + + + + + 98 + gi|396639330|pdb|2J01|A + Chain A, Structure Of The Thermus Thermophilus 70s Ribosome Complexed With Mrna, Trna And Paromomycin (Part 2 Of 4). This File Contains The 50s Subunit From Molecule I. >gi|396639355|pdb|2J03|A Chain A, Structure Of The Thermus Thermophilus 70s Ribosome Complexed With Mrna, Trna And Paromomycin (Part 4 Of 4). This File Contains The 50s Subunit From Molecule Ii. + 2J01_A + 2787 + + + 1 + 16.3517 + 8 + 47.0266 + 8 + 15 + 1948 + 1955 + 1 + 1 + 8 + 8 + 0 + 8 + CGTGAAGA + CGTGAAGA + |||||||| + + + 2 + 16.3517 + 8 + 47.0266 + 5 + 12 + 2474 + 2481 + 1 + 1 + 8 + 8 + 0 + 8 + CGTCGTGA + CGTCGTGA + |||||||| + + + + + 99 + gi|393715375|pdb|4AQX|C + Chain C, Crystal Structure Of I-Crei Complexed With Its Target Methylated At Position Plus 2 (In The B Strand) In The Presence Of Magnesium + 4AQX_C + 14 + + + 1 + 16.3517 + 8 + 47.0266 + 5 + 12 + 7 + 14 + 1 + 1 + 8 + 8 + 0 + 8 + CGTCGTGA + CGTCGTGA + |||||||| + + + + + 100 + gi|393715371|pdb|4AQU|C + Chain C, Crystal Structure Of I-Crei Complexed With Its Target Methylated At Position Plus 2 (In The B Strand) In The Presence Of Calcium + 4AQU_C + 24 + + + 1 + 16.3517 + 8 + 47.0266 + 5 + 12 + 7 + 14 + 1 + 1 + 8 + 8 + 0 + 8 + CGTCGTGA + CGTCGTGA + |||||||| + + + + + + + 8975 + 885284 + 0 + 0 + 0.710602795216363 + 1.37406312246009 + 1.30724660390929 + + + + + + diff -r 000000000000 -r a54279222d84 test-data/blast xml example2.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/blast xml example2.html Mon May 19 09:43:54 2014 -0400 @@ -0,0 +1,424 @@ + + + + + + + Blast output + + + + + + + + + + +
+ +
+
This html page seems to have been stripped by Galaxy.
+ Disable Galaxy's html sanitization feature to view the full page (see sanitize_all_html in your galaxy's universe_wsgi.ini), or download this page instead of viewing it in Galaxy. +
+
+ +
+ + + + +
+ +

Nucleotide Sequence (16 letters)

+ +
+ + + + + + + +
Query ID:Query_1
Query definition:No definition line
Query length:16
Program:BLASTN 2.2.28+
Database:/share/BlastDB/nt
+ +
+ +
+

No Hits

+
+ + +
Message:No hits found
+
+
+
+ +
+ + + + + diff -r 000000000000 -r a54279222d84 test-data/blast xml example2.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/blast xml example2.xml Mon May 19 09:43:54 2014 -0400 @@ -0,0 +1,44 @@ + + + + blastn + BLASTN 2.2.28+ + Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. + /share/BlastDB/nt + Query_1 + No definition line + 16 + + + 0.001 + 2 + -3 + 5 + 2 + L;m; + + + + + 1 + Query_1 + No definition line + 16 + + + + + 28813188 + 53027764389 + 13 + 157959578835 + 0.41 + 0.625 + 0.78 + + + No hits found + + + + diff -r 000000000000 -r a54279222d84 test-data/blast xml example3.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/blast xml example3.html Mon May 19 09:43:54 2014 -0400 @@ -0,0 +1,3530 @@ + + + + + + + Blast output + + + + + + + + + + +
+ +
+
This html page seems to have been stripped by Galaxy.
+ Disable Galaxy's html sanitization feature to view the full page (see sanitize_all_html in your galaxy's universe_wsgi.ini), or download this page instead of viewing it in Galaxy. +
+
+ +
+ + +
+

Queries

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +

Nucleotide Sequence (20 letters)

+ +
+ + + + + + + +
Query ID:Query_1
Query definition:Forward_Primer|NOST-Spec_(Genetic_ID)
Query length:20
Program:BLASTN 2.2.29+
Database:
+ +
+ +
+

No Hits

+
+ + +
Message:No hits found
+
+
+
+ +
+ +

Nucleotide Sequence (20 letters)

+ +
+ + + + + + + +
Query ID:Query_1
Query definition:Forward_Primer|NOST-Spec_(Genetic_ID)
Query length:20
Program:BLASTN 2.2.29+
Database:
+ +
+ +
+

No Hits

+
+ + +
Message:No hits found
+
+
+
+ +
+ +

Nucleotide Sequence (20 letters)

+ +
+ + + + + + + +
Query ID:Query_1
Query definition:Forward_Primer|NOST-Spec_(Genetic_ID)
Query length:20
Program:BLASTN 2.2.29+
Database:
+ +
+ + +
+

Graphic Summary

+ +
+

Distribution of 56 Blast Hits on the Query Sequence

+ +
+ Mouse-over to show defline and scores, click to show alignments +
+ +
+

Color key for alignment scores

+
+
<40
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40–50
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50–80
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80–200
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200≤
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query:
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Descriptions

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Sequences producing significant alignments:

+ + + + + + + + + + + + + + + + + + + + + +
DescriptionMax scoreTotal scoreQuery coverE valueIdentAccession
37.437.4100%7.011e-08100%Subject_3
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+

Alignments

+ +
+
+ + + +
+

DJ437711|GenBank|insert_MIR604|Corn_Event_MIR604,_Left_Border_region|-5751164067366620000

+

+ Sequence ID: Subject_3 + Length: 323 + Number of Matches: 1 +

+
+ + +
+

+ Range 1: 200 to 219 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
37.4 bits(40)0.020/20(100%)0/20(0%)Plus/Plus
+ +
Query        1  AGCGCGCAAACTAGGATAAA  20
+                ||||||||||||||||||||
+Subject    200  AGCGCGCAAACTAGGATAAA  219
+
+ +
+ +
+
+
+ +
+ +

Nucleotide Sequence (20 letters)

+ +
+ + + + + + + +
Query ID:Query_1
Query definition:Forward_Primer|NOST-Spec_(Genetic_ID)
Query length:20
Program:BLASTN 2.2.29+
Database:
+ +
+ +
+

No Hits

+
+ + +
Message:No hits found
+
+
+
+ +
+ +

Nucleotide Sequence (20 letters)

+ +
+ + + + + + + +
Query ID:Query_1
Query definition:Forward_Primer|NOST-Spec_(Genetic_ID)
Query length:20
Program:BLASTN 2.2.29+
Database:
+ +
+ +
+

No Hits

+
+ + +
Message:No hits found
+
+
+
+ +
+ +

Nucleotide Sequence (20 letters)

+ +
+ + + + + + + +
Query ID:Query_1
Query definition:Forward_Primer|NOST-Spec_(Genetic_ID)
Query length:20
Program:BLASTN 2.2.29+
Database:
+ +
+ + +
+

Graphic Summary

+ +
+

Distribution of 56 Blast Hits on the Query Sequence

+ +
+ Mouse-over to show defline and scores, click to show alignments +
+ +
+

Color key for alignment scores

+
+
<40
+
40–50
+
50–80
+
80–200
+
200≤
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+
+ +
+ +
+
query:
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2
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20
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+ + +
+
+
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+ +
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+
+
+ + + +
+

Descriptions

+ +
+

Sequences producing significant alignments:

+ + + + + + + + + + + + + + + + + + + + + +
DescriptionMax scoreTotal scoreQuery coverE valueIdentAccession
37.437.4100%7.011e-08100%Subject_6
+ +
+
+ + + +
+

Alignments

+ +
+
+ + + +
+

AB209952.1|GenBank|insert_GTS-40-3-2|Glycine_max_transgenic_cp4epsps_gene_for_5-enol-pyruvylshikimate-3-phospate_synthase_class_2_precursor,_complete_cds|-9105899556052450000

+

+ Sequence ID: Subject_6 + Length: 2457 + Number of Matches: 1 +

+
+ + +
+

+ Range 1: 2119 to 2138 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
37.4 bits(40)0.020/20(100%)0/20(0%)Plus/Plus
+ +
Query        1  AGCGCGCAAACTAGGATAAA  20
+                ||||||||||||||||||||
+Subject   2119  AGCGCGCAAACTAGGATAAA  2138
+
+ +
+ +
+
+
+ +
+ +

Nucleotide Sequence (20 letters)

+ +
+ + + + + + + +
Query ID:Query_1
Query definition:Forward_Primer|NOST-Spec_(Genetic_ID)
Query length:20
Program:BLASTN 2.2.29+
Database:
+ +
+ +
+

No Hits

+
+ + +
Message:No hits found
+
+
+
+ +
+ +

Nucleotide Sequence (20 letters)

+ +
+ + + + + + + +
Query ID:Query_1
Query definition:Forward_Primer|NOST-Spec_(Genetic_ID)
Query length:20
Program:BLASTN 2.2.29+
Database:
+ +
+ +
+

No Hits

+
+ + +
Message:No hits found
+
+
+
+ +
+ +

Nucleotide Sequence (20 letters)

+ +
+ + + + + + + +
Query ID:Query_1
Query definition:Forward_Primer|NOST-Spec_(Genetic_ID)
Query length:20
Program:BLASTN 2.2.29+
Database:
+ +
+ +
+

No Hits

+
+ + +
Message:No hits found
+
+
+
+ +
+ +

Nucleotide Sequence (20 letters)

+ +
+ + + + + + + +
Query ID:Query_1
Query definition:Forward_Primer|NOST-Spec_(Genetic_ID)
Query length:20
Program:BLASTN 2.2.29+
Database:
+ +
+ +
+

No Hits

+
+ + +
Message:No hits found
+
+
+
+ +
+ +

Nucleotide Sequence (20 letters)

+ +
+ + + + + + + +
Query ID:Query_1
Query definition:Forward_Primer|NOST-Spec_(Genetic_ID)
Query length:20
Program:BLASTN 2.2.29+
Database:
+ +
+ +
+

No Hits

+
+ + +
Message:No hits found
+
+
+
+ +
+ +

Nucleotide Sequence (20 letters)

+ +
+ + + + + + + +
Query ID:Query_1
Query definition:Forward_Primer|NOST-Spec_(Genetic_ID)
Query length:20
Program:BLASTN 2.2.29+
Database:
+ +
+ +
+

No Hits

+
+ + +
Message:No hits found
+
+
+
+ +
+ +

Nucleotide Sequence (20 letters)

+ +
+ + + + + + + +
Query ID:Query_1
Query definition:Forward_Primer|NOST-Spec_(Genetic_ID)
Query length:20
Program:BLASTN 2.2.29+
Database:
+ +
+ +
+

No Hits

+
+ + +
Message:No hits found
+
+
+
+ +
+ +

Nucleotide Sequence (20 letters)

+ +
+ + + + + + + +
Query ID:Query_1
Query definition:Forward_Primer|NOST-Spec_(Genetic_ID)
Query length:20
Program:BLASTN 2.2.29+
Database:
+ +
+ +
+

No Hits

+
+ + +
Message:No hits found
+
+
+
+ +
+ +

Nucleotide Sequence (20 letters)

+ +
+ + + + + + + +
Query ID:Query_1
Query definition:Forward_Primer|NOST-Spec_(Genetic_ID)
Query length:20
Program:BLASTN 2.2.29+
Database:
+ +
+ +
+

No Hits

+
+ + +
Message:No hits found
+
+
+
+ +
+ +

Nucleotide Sequence (20 letters)

+ +
+ + + + + + + +
Query ID:Query_1
Query definition:Forward_Primer|NOST-Spec_(Genetic_ID)
Query length:20
Program:BLASTN 2.2.29+
Database:
+ +
+ +
+

No Hits

+
+ + +
Message:No hits found
+
+
+
+ +
+ +

Nucleotide Sequence (20 letters)

+ +
+ + + + + + + +
Query ID:Query_1
Query definition:Forward_Primer|NOST-Spec_(Genetic_ID)
Query length:20
Program:BLASTN 2.2.29+
Database:
+ +
+ +
+

No Hits

+
+ + +
Message:No hits found
+
+
+
+ +
+ +

Nucleotide Sequence (20 letters)

+ +
+ + + + + + + +
Query ID:Query_1
Query definition:Forward_Primer|NOST-Spec_(Genetic_ID)
Query length:20
Program:BLASTN 2.2.29+
Database:
+ +
+ + +
+

Graphic Summary

+ +
+

Distribution of 56 Blast Hits on the Query Sequence

+ +
+ Mouse-over to show defline and scores, click to show alignments +
+ +
+

Color key for alignment scores

+
+
<40
+
40–50
+
50–80
+
80–200
+
200≤
+
+
+ +
+ +
+
query:
+
+
+
+
2
+
+
+
4
+
+
+
6
+
+
+
8
+
+
+
10
+
+
+
12
+
+
+
14
+
+
+
16
+
+
+
18
+
+
+
20
+
+
+
+
+
+ + +
+
+
+
+
+ +
+
+
+
+ + + +
+

Descriptions

+ +
+

Sequences producing significant alignments:

+ + + + + + + + + + + + + + + + + + + + + +
DescriptionMax scoreTotal scoreQuery coverE valueIdentAccession
31.931.985%2.981e-06100%Subject_2
+ +
+
+ + + +
+

Alignments

+ +
+
+ + + +
+

AJ308515.1|GenBank|insert_GTS-40-3-2|Synthetic_construct_for_NOS_3'UTR/plant_junction_region.|-9105899556052450000

+

+ Sequence ID: Subject_2 + Length: 1045 + Number of Matches: 1 +

+
+ + +
+

+ Range 1: 2 to 18 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
31.9 bits(34)0.017/17(100%)0/17(0%)Plus/Plus
+ +
Query        4  GCGCGGTGTCATCTATG  20
+                |||||||||||||||||
+Subject      2  GCGCGGTGTCATCTATG  18
+
+ +
+ +
+
+
+ +
+ +

Nucleotide Sequence (20 letters)

+ +
+ + + + + + + +
Query ID:Query_1
Query definition:Forward_Primer|NOST-Spec_(Genetic_ID)
Query length:20
Program:BLASTN 2.2.29+
Database:
+ +
+ + +
+

Graphic Summary

+ +
+

Distribution of 56 Blast Hits on the Query Sequence

+ +
+ Mouse-over to show defline and scores, click to show alignments +
+ +
+

Color key for alignment scores

+
+
<40
+
40–50
+
50–80
+
80–200
+
200≤
+
+
+ +
+ +
+
query:
+
+
+
+
2
+
+
+
4
+
+
+
6
+
+
+
8
+
+
+
10
+
+
+
12
+
+
+
14
+
+
+
16
+
+
+
18
+
+
+
20
+
+
+
+
+
+ + +
+
+
+
+ +
+
+
+
+ + + +
+

Descriptions

+ +
+

Sequences producing significant alignments:

+ + + + + + + + + + + + + + + + + + + + + +
DescriptionMax scoreTotal scoreQuery coverE valueIdentAccession
37.437.4100%7.011e-08100%Subject_3
+ +
+
+ + + +
+

Alignments

+ +
+
+ + + +
+

DJ437711|GenBank|insert_MIR604|Corn_Event_MIR604,_Left_Border_region|-5751164067366620000

+

+ Sequence ID: Subject_3 + Length: 323 + Number of Matches: 1 +

+
+ + +
+

+ Range 1: 224 to 243 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
37.4 bits(40)0.020/20(100%)0/20(0%)Plus/Plus
+ +
Query        1  CGCGCGCGGTGTCATCTATG  20
+                ||||||||||||||||||||
+Subject    224  CGCGCGCGGTGTCATCTATG  243
+
+ +
+ +
+
+
+ +
+ +

Nucleotide Sequence (20 letters)

+ +
+ + + + + + + +
Query ID:Query_1
Query definition:Forward_Primer|NOST-Spec_(Genetic_ID)
Query length:20
Program:BLASTN 2.2.29+
Database:
+ +
+ +
+

No Hits

+
+ + +
Message:No hits found
+
+
+
+ +
+ +

Nucleotide Sequence (20 letters)

+ +
+ + + + + + + +
Query ID:Query_1
Query definition:Forward_Primer|NOST-Spec_(Genetic_ID)
Query length:20
Program:BLASTN 2.2.29+
Database:
+ +
+ +
+

No Hits

+
+ + +
Message:No hits found
+
+
+
+ +
+ +

Nucleotide Sequence (20 letters)

+ +
+ + + + + + + +
Query ID:Query_1
Query definition:Forward_Primer|NOST-Spec_(Genetic_ID)
Query length:20
Program:BLASTN 2.2.29+
Database:
+ +
+ + +
+

Graphic Summary

+ +
+

Distribution of 56 Blast Hits on the Query Sequence

+ +
+ Mouse-over to show defline and scores, click to show alignments +
+ +
+

Color key for alignment scores

+
+
<40
+
40–50
+
50–80
+
80–200
+
200≤
+
+
+ +
+ +
+
query:
+
+
+
+
2
+
+
+
4
+
+
+
6
+
+
+
8
+
+
+
10
+
+
+
12
+
+
+
14
+
+
+
16
+
+
+
18
+
+
+
20
+
+
+
+
+
+ + +
+
+
+
+ +
+
+
+
+ + + +
+

Descriptions

+ +
+

Sequences producing significant alignments:

+ + + + + + + + + + + + + + + + + + + + + +
DescriptionMax scoreTotal scoreQuery coverE valueIdentAccession
37.437.4100%7.011e-08100%Subject_6
+ +
+
+ + + +
+

Alignments

+ +
+
+ + + +
+

AB209952.1|GenBank|insert_GTS-40-3-2|Glycine_max_transgenic_cp4epsps_gene_for_5-enol-pyruvylshikimate-3-phospate_synthase_class_2_precursor,_complete_cds|-9105899556052450000

+

+ Sequence ID: Subject_6 + Length: 2457 + Number of Matches: 1 +

+
+ + +
+

+ Range 1: 2143 to 2162 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
37.4 bits(40)0.020/20(100%)0/20(0%)Plus/Plus
+ +
Query        1  CGCGCGCGGTGTCATCTATG  20
+                ||||||||||||||||||||
+Subject   2143  CGCGCGCGGTGTCATCTATG  2162
+
+ +
+ +
+
+
+ +
+ +

Nucleotide Sequence (20 letters)

+ +
+ + + + + + + +
Query ID:Query_1
Query definition:Forward_Primer|NOST-Spec_(Genetic_ID)
Query length:20
Program:BLASTN 2.2.29+
Database:
+ +
+ +
+

No Hits

+
+ + +
Message:No hits found
+
+
+
+ +
+ +

Nucleotide Sequence (20 letters)

+ +
+ + + + + + + +
Query ID:Query_1
Query definition:Forward_Primer|NOST-Spec_(Genetic_ID)
Query length:20
Program:BLASTN 2.2.29+
Database:
+ +
+ +
+

No Hits

+
+ + +
Message:No hits found
+
+
+
+ +
+ +

Nucleotide Sequence (24 letters)

+ +
+ + + + + + + +
Query ID:Query_1
Query definition:Forward_Primer|NOST-Spec_(Genetic_ID)
Query length:20
Program:BLASTN 2.2.29+
Database:
+ +
+ +
+

No Hits

+
+ + +
Message:No hits found
+
+
+
+ +
+ +

Nucleotide Sequence (24 letters)

+ +
+ + + + + + + +
Query ID:Query_1
Query definition:Forward_Primer|NOST-Spec_(Genetic_ID)
Query length:20
Program:BLASTN 2.2.29+
Database:
+ +
+ +
+

No Hits

+
+ + +
Message:No hits found
+
+
+
+ +
+ +

Nucleotide Sequence (24 letters)

+ +
+ + + + + + + +
Query ID:Query_1
Query definition:Forward_Primer|NOST-Spec_(Genetic_ID)
Query length:20
Program:BLASTN 2.2.29+
Database:
+ +
+ +
+

No Hits

+
+ + +
Message:No hits found
+
+
+
+ +
+ +

Nucleotide Sequence (24 letters)

+ +
+ + + + + + + +
Query ID:Query_1
Query definition:Forward_Primer|NOST-Spec_(Genetic_ID)
Query length:20
Program:BLASTN 2.2.29+
Database:
+ +
+ +
+

No Hits

+
+ + +
Message:No hits found
+
+
+
+ +
+ +

Nucleotide Sequence (24 letters)

+ +
+ + + + + + + +
Query ID:Query_1
Query definition:Forward_Primer|NOST-Spec_(Genetic_ID)
Query length:20
Program:BLASTN 2.2.29+
Database:
+ +
+ +
+

No Hits

+
+ + +
Message:No hits found
+
+
+
+ +
+ +

Nucleotide Sequence (24 letters)

+ +
+ + + + + + + +
Query ID:Query_1
Query definition:Forward_Primer|NOST-Spec_(Genetic_ID)
Query length:20
Program:BLASTN 2.2.29+
Database:
+ +
+ +
+

No Hits

+
+ + +
Message:No hits found
+
+
+
+ +
+ +

Nucleotide Sequence (24 letters)

+ +
+ + + + + + + +
Query ID:Query_1
Query definition:Forward_Primer|NOST-Spec_(Genetic_ID)
Query length:20
Program:BLASTN 2.2.29+
Database:
+ +
+ +
+

No Hits

+
+ + +
Message:No hits found
+
+
+
+ +
+ +

Nucleotide Sequence (24 letters)

+ +
+ + + + + + + +
Query ID:Query_1
Query definition:Forward_Primer|NOST-Spec_(Genetic_ID)
Query length:20
Program:BLASTN 2.2.29+
Database:
+ +
+ +
+

No Hits

+
+ + +
Message:No hits found
+
+
+
+ +
+ +

Nucleotide Sequence (20 letters)

+ +
+ + + + + + + +
Query ID:Query_1
Query definition:Forward_Primer|NOST-Spec_(Genetic_ID)
Query length:20
Program:BLASTN 2.2.29+
Database:
+ +
+ +
+

No Hits

+
+ + +
Message:No hits found
+
+
+
+ +
+ +

Nucleotide Sequence (20 letters)

+ +
+ + + + + + + +
Query ID:Query_1
Query definition:Forward_Primer|NOST-Spec_(Genetic_ID)
Query length:20
Program:BLASTN 2.2.29+
Database:
+ +
+ +
+

No Hits

+
+ + +
Message:No hits found
+
+
+
+ +
+ +

Nucleotide Sequence (20 letters)

+ +
+ + + + + + + +
Query ID:Query_1
Query definition:Forward_Primer|NOST-Spec_(Genetic_ID)
Query length:20
Program:BLASTN 2.2.29+
Database:
+ +
+ +
+

No Hits

+
+ + +
Message:No hits found
+
+
+
+ +
+ +

Nucleotide Sequence (20 letters)

+ +
+ + + + + + + +
Query ID:Query_1
Query definition:Forward_Primer|NOST-Spec_(Genetic_ID)
Query length:20
Program:BLASTN 2.2.29+
Database:
+ +
+ +
+

No Hits

+
+ + +
Message:No hits found
+
+
+
+ +
+ +

Nucleotide Sequence (20 letters)

+ +
+ + + + + + + +
Query ID:Query_1
Query definition:Forward_Primer|NOST-Spec_(Genetic_ID)
Query length:20
Program:BLASTN 2.2.29+
Database:
+ +
+ +
+

No Hits

+
+ + +
Message:No hits found
+
+
+
+ +
+ +

Nucleotide Sequence (20 letters)

+ +
+ + + + + + + +
Query ID:Query_1
Query definition:Forward_Primer|NOST-Spec_(Genetic_ID)
Query length:20
Program:BLASTN 2.2.29+
Database:
+ +
+ +
+

No Hits

+
+ + +
Message:No hits found
+
+
+
+ +
+ +

Nucleotide Sequence (20 letters)

+ +
+ + + + + + + +
Query ID:Query_1
Query definition:Forward_Primer|NOST-Spec_(Genetic_ID)
Query length:20
Program:BLASTN 2.2.29+
Database:
+ +
+ +
+

No Hits

+
+ + +
Message:No hits found
+
+
+
+ +
+ +

Nucleotide Sequence (20 letters)

+ +
+ + + + + + + +
Query ID:Query_1
Query definition:Forward_Primer|NOST-Spec_(Genetic_ID)
Query length:20
Program:BLASTN 2.2.29+
Database:
+ +
+ +
+

No Hits

+
+ + +
Message:No hits found
+
+
+
+ +
+ +

Nucleotide Sequence (25 letters)

+ +
+ + + + + + + +
Query ID:Query_1
Query definition:Forward_Primer|NOST-Spec_(Genetic_ID)
Query length:20
Program:BLASTN 2.2.29+
Database:
+ +
+ +
+

No Hits

+
+ + +
Message:No hits found
+
+
+
+ +
+ +

Nucleotide Sequence (25 letters)

+ +
+ + + + + + + +
Query ID:Query_1
Query definition:Forward_Primer|NOST-Spec_(Genetic_ID)
Query length:20
Program:BLASTN 2.2.29+
Database:
+ +
+ +
+

No Hits

+
+ + +
Message:No hits found
+
+
+
+ +
+ +

Nucleotide Sequence (25 letters)

+ +
+ + + + + + + +
Query ID:Query_1
Query definition:Forward_Primer|NOST-Spec_(Genetic_ID)
Query length:20
Program:BLASTN 2.2.29+
Database:
+ +
+ +
+

No Hits

+
+ + +
Message:No hits found
+
+
+
+ +
+ +

Nucleotide Sequence (25 letters)

+ +
+ + + + + + + +
Query ID:Query_1
Query definition:Forward_Primer|NOST-Spec_(Genetic_ID)
Query length:20
Program:BLASTN 2.2.29+
Database:
+ +
+ +
+

No Hits

+
+ + +
Message:No hits found
+
+
+
+ +
+ +

Nucleotide Sequence (25 letters)

+ +
+ + + + + + + +
Query ID:Query_1
Query definition:Forward_Primer|NOST-Spec_(Genetic_ID)
Query length:20
Program:BLASTN 2.2.29+
Database:
+ +
+ +
+

No Hits

+
+ + +
Message:No hits found
+
+
+
+ +
+ +

Nucleotide Sequence (25 letters)

+ +
+ + + + + + + +
Query ID:Query_1
Query definition:Forward_Primer|NOST-Spec_(Genetic_ID)
Query length:20
Program:BLASTN 2.2.29+
Database:
+ +
+ +
+

No Hits

+
+ + +
Message:No hits found
+
+
+
+ +
+ +

Nucleotide Sequence (25 letters)

+ +
+ + + + + + + +
Query ID:Query_1
Query definition:Forward_Primer|NOST-Spec_(Genetic_ID)
Query length:20
Program:BLASTN 2.2.29+
Database:
+ +
+ + +
+

Graphic Summary

+ +
+

Distribution of 56 Blast Hits on the Query Sequence

+ +
+ Mouse-over to show defline and scores, click to show alignments +
+ +
+

Color key for alignment scores

+
+
<40
+
40–50
+
50–80
+
80–200
+
200≤
+
+
+ +
+ +
+
query:
+
+
+
+
3
+
+
+
6
+
+
+
9
+
+
+
12
+
+
+
15
+
+
+
18
+
+
+
21
+
+
+
24
+
+
+
25
+
+
+
+
+
+ + +
+
+
+
+ +
+
+
+
+ + + +
+

Descriptions

+ +
+

Sequences producing significant alignments:

+ + + + + + + + + + + + + + + + + + + + + +
DescriptionMax scoreTotal scoreQuery coverE valueIdentAccession
37.437.4100%9.338e-0892%Subject_7
+ +
+
+ + + +
+

Alignments

+ +
+
+ + + +
+

AY326434|GenBank|insert_MON810|Synthetic_construct_truncated_CRYIA(b)_(cryIA(b))_gene,_partial_CDS|-2635190737607180000

+

+ Sequence ID: Subject_7 + Length: 4180 + Number of Matches: 1 +

+
+ + +
+

+ Range 1: 1541 to 1565 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
37.4 bits(40)0.023/25(92%)0/25(0%)Plus/Plus
+ +
Query        1  ACATGAACAGCGCCTTGACCACAGC  25
+                |||||||||||||| ||||||| ||
+Subject   1541  ACATGAACAGCGCCCTGACCACCGC  1565
+
+ +
+ +
+
+
+ +
+ +

Nucleotide Sequence (25 letters)

+ +
+ + + + + + + +
Query ID:Query_1
Query definition:Forward_Primer|NOST-Spec_(Genetic_ID)
Query length:20
Program:BLASTN 2.2.29+
Database:
+ +
+ + +
+

Graphic Summary

+ +
+

Distribution of 56 Blast Hits on the Query Sequence

+ +
+ Mouse-over to show defline and scores, click to show alignments +
+ +
+

Color key for alignment scores

+
+
<40
+
40–50
+
50–80
+
80–200
+
200≤
+
+
+ +
+ +
+
query:
+
+
+
+
3
+
+
+
6
+
+
+
9
+
+
+
12
+
+
+
15
+
+
+
18
+
+
+
21
+
+
+
24
+
+
+
25
+
+
+
+
+
+ + +
+
+
+
+ +
+
+
+
+ + + +
+

Descriptions

+ +
+

Sequences producing significant alignments:

+ + + + + + + + + + + + + + + + + + + + + +
DescriptionMax scoreTotal scoreQuery coverE valueIdentAccession
37.437.4100%9.338e-0892%Subject_8
+ +
+
+ + + +
+

Alignments

+ +
+
+ + + +
+

EUG|RIKILT|plasmid_pV-ZMBK07|plasmid_pV-ZMBK07|-2635190737607180000

+

+ Sequence ID: Subject_8 + Length: 4983 + Number of Matches: 1 +

+
+ + +
+

+ Range 1: 2344 to 2368 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
37.4 bits(40)0.023/25(92%)0/25(0%)Plus/Plus
+ +
Query        1  ACATGAACAGCGCCTTGACCACAGC  25
+                |||||||||||||| ||||||| ||
+Subject   2344  ACATGAACAGCGCCCTGACCACCGC  2368
+
+ +
+ +
+
+
+ +
+ +

Nucleotide Sequence (74 letters)

+ +
+ + + + + + + +
Query ID:Query_1
Query definition:Forward_Primer|NOST-Spec_(Genetic_ID)
Query length:20
Program:BLASTN 2.2.29+
Database:
+ +
+ +
+

No Hits

+
+ + +
Message:No hits found
+
+
+
+ +
+ +

Nucleotide Sequence (74 letters)

+ +
+ + + + + + + +
Query ID:Query_1
Query definition:Forward_Primer|NOST-Spec_(Genetic_ID)
Query length:20
Program:BLASTN 2.2.29+
Database:
+ +
+ +
+

No Hits

+
+ + +
Message:No hits found
+
+
+
+ +
+ +

Nucleotide Sequence (74 letters)

+ +
+ + + + + + + +
Query ID:Query_1
Query definition:Forward_Primer|NOST-Spec_(Genetic_ID)
Query length:20
Program:BLASTN 2.2.29+
Database:
+ +
+ +
+

No Hits

+
+ + +
Message:No hits found
+
+
+
+ +
+ +

Nucleotide Sequence (74 letters)

+ +
+ + + + + + + +
Query ID:Query_1
Query definition:Forward_Primer|NOST-Spec_(Genetic_ID)
Query length:20
Program:BLASTN 2.2.29+
Database:
+ +
+ +
+

No Hits

+
+ + +
Message:No hits found
+
+
+
+ +
+ +

Nucleotide Sequence (74 letters)

+ +
+ + + + + + + +
Query ID:Query_1
Query definition:Forward_Primer|NOST-Spec_(Genetic_ID)
Query length:20
Program:BLASTN 2.2.29+
Database:
+ +
+ +
+

No Hits

+
+ + +
Message:No hits found
+
+
+
+ +
+ +

Nucleotide Sequence (74 letters)

+ +
+ + + + + + + +
Query ID:Query_1
Query definition:Forward_Primer|NOST-Spec_(Genetic_ID)
Query length:20
Program:BLASTN 2.2.29+
Database:
+ +
+ +
+

No Hits

+
+ + +
Message:No hits found
+
+
+
+ +
+ +

Nucleotide Sequence (74 letters)

+ +
+ + + + + + + +
Query ID:Query_1
Query definition:Forward_Primer|NOST-Spec_(Genetic_ID)
Query length:20
Program:BLASTN 2.2.29+
Database:
+ +
+ + +
+

Graphic Summary

+ +
+

Distribution of 56 Blast Hits on the Query Sequence

+ +
+ Mouse-over to show defline and scores, click to show alignments +
+ +
+

Color key for alignment scores

+
+
<40
+
40–50
+
50–80
+
80–200
+
200≤
+
+
+ +
+ +
+
query:
+
+
+
+
8
+
+
+
16
+
+
+
24
+
+
+
32
+
+
+
40
+
+
+
48
+
+
+
56
+
+
+
64
+
+
+
72
+
+
+
 
+
74
+
+
+
+
+
+ + +
+
+
+
+ +
+
+
+
+ + + +
+

Descriptions

+ +
+

Sequences producing significant alignments:

+ + + + + + + + + + + + + + + + + + + + + +
DescriptionMax scoreTotal scoreQuery coverE valueIdentAccession
89.789.7100%6.629e-2386%Subject_7
+ +
+
+ + + +
+

Alignments

+ +
+
+ + + +
+

AY326434|GenBank|insert_MON810|Synthetic_construct_truncated_CRYIA(b)_(cryIA(b))_gene,_partial_CDS|-2635190737607180000

+

+ Sequence ID: Subject_7 + Length: 4180 + Number of Matches: 1 +

+
+ + +
+

+ Range 1: 1516 to 1589 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
89.7 bits(98)0.064/74(86%)0/74(0%)Plus/Plus
+ +
Query        1  GAGGAAATGCGTATTCAATTCAACGACATGAACAGCGCCTTGACCACAGCTATCCCATTGTTCGCAGTCCAGAA  74
+                ||||| ||||| || || ||||||||||||||||||||| ||||||| || |||||| | ||||| ||||||||
+Subject   1516  GAGGAGATGCGCATCCAGTTCAACGACATGAACAGCGCCCTGACCACCGCCATCCCACTCTTCGCCGTCCAGAA  1589
+
+ +
+ +
+
+
+ +
+ +

Nucleotide Sequence (74 letters)

+ +
+ + + + + + + +
Query ID:Query_1
Query definition:Forward_Primer|NOST-Spec_(Genetic_ID)
Query length:20
Program:BLASTN 2.2.29+
Database:
+ +
+ + +
+

Graphic Summary

+ +
+

Distribution of 56 Blast Hits on the Query Sequence

+ +
+ Mouse-over to show defline and scores, click to show alignments +
+ +
+

Color key for alignment scores

+
+
<40
+
40–50
+
50–80
+
80–200
+
200≤
+
+
+ +
+ +
+
query:
+
+
+
+
8
+
+
+
16
+
+
+
24
+
+
+
32
+
+
+
40
+
+
+
48
+
+
+
56
+
+
+
64
+
+
+
72
+
+
+
 
+
74
+
+
+
+
+
+ + +
+
+
+
+ +
+
+
+
+ + + +
+

Descriptions

+ +
+

Sequences producing significant alignments:

+ + + + + + + + + + + + + + + + + + + + + +
DescriptionMax scoreTotal scoreQuery coverE valueIdentAccession
89.789.7100%6.629e-2386%Subject_8
+ +
+
+ + + +
+

Alignments

+ +
+
+ + + +
+

EUG|RIKILT|plasmid_pV-ZMBK07|plasmid_pV-ZMBK07|-2635190737607180000

+

+ Sequence ID: Subject_8 + Length: 4983 + Number of Matches: 1 +

+
+ + +
+

+ Range 1: 2319 to 2392 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
89.7 bits(98)0.064/74(86%)0/74(0%)Plus/Plus
+ +
Query        1  GAGGAAATGCGTATTCAATTCAACGACATGAACAGCGCCTTGACCACAGCTATCCCATTGTTCGCAGTCCAGAA  74
+                ||||| ||||| || || ||||||||||||||||||||| ||||||| || |||||| | ||||| ||||||||
+Subject   2319  GAGGAGATGCGCATCCAGTTCAACGACATGAACAGCGCCCTGACCACCGCCATCCCACTCTTCGCCGTCCAGAA  2392
+
+ +
+ +
+
+
+ +
+ + + + + diff -r 000000000000 -r a54279222d84 test-data/blast xml example3.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/blast xml example3.xml Mon May 19 09:43:54 2014 -0400 @@ -0,0 +1,1387 @@ + + + + blastn + BLASTN 2.2.29+ + Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. + + Query_1 + Forward_Primer|NOST-Spec_(Genetic_ID) + 20 + + + 0.001 + 2 + -3 + 5 + 2 + L;m; + + + + + 1 + Query_1 + Forward_Primer|NOST-Spec_(Genetic_ID) + 20 + + + + + 0 + 0 + 8 + 12312 + 0.41 + 0.625 + 0.78 + + + No hits found + + + 2 + Query_1 + Forward_Primer|NOST-Spec_(Genetic_ID) + 20 + + + + + 0 + 0 + 8 + 12312 + 0.41 + 0.625 + 0.78 + + + No hits found + + + 3 + Query_1 + Forward_Primer|NOST-Spec_(Genetic_ID) + 20 + + + 1 + Subject_3 + DJ437711|GenBank|insert_MIR604|Corn_Event_MIR604,_Left_Border_region|-5751164067366620000 + Subject_3 + 323 + + + 1 + 37.3537 + 40 + 7.01052e-08 + 1 + 20 + 200 + 219 + 1 + 1 + 20 + 20 + 0 + 20 + AGCGCGCAAACTAGGATAAA + AGCGCGCAAACTAGGATAAA + |||||||||||||||||||| + + + + + + + 0 + 0 + 8 + 12312 + 0.41 + 0.625 + 0.78 + + + + + 4 + Query_1 + Forward_Primer|NOST-Spec_(Genetic_ID) + 20 + + + + + 0 + 0 + 8 + 12312 + 0.41 + 0.625 + 0.78 + + + No hits found + + + 5 + Query_1 + Forward_Primer|NOST-Spec_(Genetic_ID) + 20 + + + + + 0 + 0 + 8 + 12312 + 0.41 + 0.625 + 0.78 + + + No hits found + + + 6 + Query_1 + Forward_Primer|NOST-Spec_(Genetic_ID) + 20 + + + 1 + Subject_6 + AB209952.1|GenBank|insert_GTS-40-3-2|Glycine_max_transgenic_cp4epsps_gene_for_5-enol-pyruvylshikimate-3-phospate_synthase_class_2_precursor,_complete_cds|-9105899556052450000 + Subject_6 + 2457 + + + 1 + 37.3537 + 40 + 7.01052e-08 + 1 + 20 + 2119 + 2138 + 1 + 1 + 20 + 20 + 0 + 20 + AGCGCGCAAACTAGGATAAA + AGCGCGCAAACTAGGATAAA + |||||||||||||||||||| + + + + + + + 0 + 0 + 8 + 12312 + 0.41 + 0.625 + 0.78 + + + + + 7 + Query_1 + Forward_Primer|NOST-Spec_(Genetic_ID) + 20 + + + + + 0 + 0 + 8 + 12312 + 0.41 + 0.625 + 0.78 + + + No hits found + + + 8 + Query_1 + Forward_Primer|NOST-Spec_(Genetic_ID) + 20 + + + + + 0 + 0 + 8 + 12312 + 0.41 + 0.625 + 0.78 + + + No hits found + + + 9 + Query_2 + Reverse_Primer|NOST-Spec_(Genetic_ID) + 20 + + + + + 0 + 0 + 8 + 12312 + 0.41 + 0.625 + 0.78 + + + No hits found + + + 10 + Query_2 + Reverse_Primer|NOST-Spec_(Genetic_ID) + 20 + + + + + 0 + 0 + 8 + 12312 + 0.41 + 0.625 + 0.78 + + + No hits found + + + 11 + Query_2 + Reverse_Primer|NOST-Spec_(Genetic_ID) + 20 + + + + + 0 + 0 + 8 + 12312 + 0.41 + 0.625 + 0.78 + + + No hits found + + + 12 + Query_2 + Reverse_Primer|NOST-Spec_(Genetic_ID) + 20 + + + + + 0 + 0 + 8 + 12312 + 0.41 + 0.625 + 0.78 + + + No hits found + + + 13 + Query_2 + Reverse_Primer|NOST-Spec_(Genetic_ID) + 20 + + + + + 0 + 0 + 8 + 12312 + 0.41 + 0.625 + 0.78 + + + No hits found + + + 14 + Query_2 + Reverse_Primer|NOST-Spec_(Genetic_ID) + 20 + + + + + 0 + 0 + 8 + 12312 + 0.41 + 0.625 + 0.78 + + + No hits found + + + 15 + Query_2 + Reverse_Primer|NOST-Spec_(Genetic_ID) + 20 + + + + + 0 + 0 + 8 + 12312 + 0.41 + 0.625 + 0.78 + + + No hits found + + + 16 + Query_2 + Reverse_Primer|NOST-Spec_(Genetic_ID) + 20 + + + + + 0 + 0 + 8 + 12312 + 0.41 + 0.625 + 0.78 + + + No hits found + + + 17 + Query_3 + Probe|NOST-Spec_(Genetic_ID) + 20 + + + + + 0 + 0 + 8 + 12312 + 0.41 + 0.625 + 0.78 + + + No hits found + + + 18 + Query_3 + Probe|NOST-Spec_(Genetic_ID) + 20 + + + 1 + Subject_2 + AJ308515.1|GenBank|insert_GTS-40-3-2|Synthetic_construct_for_NOS_3'UTR/plant_junction_region.|-9105899556052450000 + Subject_2 + 1045 + + + 1 + 31.9436 + 34 + 2.98095e-06 + 4 + 20 + 2 + 18 + 1 + 1 + 17 + 17 + 0 + 17 + GCGCGGTGTCATCTATG + GCGCGGTGTCATCTATG + ||||||||||||||||| + + + + + + + 0 + 0 + 8 + 12312 + 0.41 + 0.625 + 0.78 + + + + + 19 + Query_3 + Probe|NOST-Spec_(Genetic_ID) + 20 + + + 1 + Subject_3 + DJ437711|GenBank|insert_MIR604|Corn_Event_MIR604,_Left_Border_region|-5751164067366620000 + Subject_3 + 323 + + + 1 + 37.3537 + 40 + 7.01052e-08 + 1 + 20 + 224 + 243 + 1 + 1 + 20 + 20 + 0 + 20 + CGCGCGCGGTGTCATCTATG + CGCGCGCGGTGTCATCTATG + |||||||||||||||||||| + + + + + + + 0 + 0 + 8 + 12312 + 0.41 + 0.625 + 0.78 + + + + + 20 + Query_3 + Probe|NOST-Spec_(Genetic_ID) + 20 + + + + + 0 + 0 + 8 + 12312 + 0.41 + 0.625 + 0.78 + + + No hits found + + + 21 + Query_3 + Probe|NOST-Spec_(Genetic_ID) + 20 + + + + + 0 + 0 + 8 + 12312 + 0.41 + 0.625 + 0.78 + + + No hits found + + + 22 + Query_3 + Probe|NOST-Spec_(Genetic_ID) + 20 + + + 1 + Subject_6 + AB209952.1|GenBank|insert_GTS-40-3-2|Glycine_max_transgenic_cp4epsps_gene_for_5-enol-pyruvylshikimate-3-phospate_synthase_class_2_precursor,_complete_cds|-9105899556052450000 + Subject_6 + 2457 + + + 1 + 37.3537 + 40 + 7.01052e-08 + 1 + 20 + 2143 + 2162 + 1 + 1 + 20 + 20 + 0 + 20 + CGCGCGCGGTGTCATCTATG + CGCGCGCGGTGTCATCTATG + |||||||||||||||||||| + + + + + + + 0 + 0 + 8 + 12312 + 0.41 + 0.625 + 0.78 + + + + + 23 + Query_3 + Probe|NOST-Spec_(Genetic_ID) + 20 + + + + + 0 + 0 + 8 + 12312 + 0.41 + 0.625 + 0.78 + + + No hits found + + + 24 + Query_3 + Probe|NOST-Spec_(Genetic_ID) + 20 + + + + + 0 + 0 + 8 + 12312 + 0.41 + 0.625 + 0.78 + + + No hits found + + + 25 + Query_4 + Forward_Primer|QL-ELE-Bt-F1(mod)/Bt-R + 24 + + + + + 0 + 0 + 9 + 15375 + 0.41 + 0.625 + 0.78 + + + No hits found + + + 26 + Query_4 + Forward_Primer|QL-ELE-Bt-F1(mod)/Bt-R + 24 + + + + + 0 + 0 + 9 + 15375 + 0.41 + 0.625 + 0.78 + + + No hits found + + + 27 + Query_4 + Forward_Primer|QL-ELE-Bt-F1(mod)/Bt-R + 24 + + + + + 0 + 0 + 9 + 15375 + 0.41 + 0.625 + 0.78 + + + No hits found + + + 28 + Query_4 + Forward_Primer|QL-ELE-Bt-F1(mod)/Bt-R + 24 + + + + + 0 + 0 + 9 + 15375 + 0.41 + 0.625 + 0.78 + + + No hits found + + + 29 + Query_4 + Forward_Primer|QL-ELE-Bt-F1(mod)/Bt-R + 24 + + + + + 0 + 0 + 9 + 15375 + 0.41 + 0.625 + 0.78 + + + No hits found + + + 30 + Query_4 + Forward_Primer|QL-ELE-Bt-F1(mod)/Bt-R + 24 + + + + + 0 + 0 + 9 + 15375 + 0.41 + 0.625 + 0.78 + + + No hits found + + + 31 + Query_4 + Forward_Primer|QL-ELE-Bt-F1(mod)/Bt-R + 24 + + + + + 0 + 0 + 9 + 15375 + 0.41 + 0.625 + 0.78 + + + No hits found + + + 32 + Query_4 + Forward_Primer|QL-ELE-Bt-F1(mod)/Bt-R + 24 + + + + + 0 + 0 + 9 + 15375 + 0.41 + 0.625 + 0.78 + + + No hits found + + + 33 + Query_5 + Reverse_Primer|QL-ELE-Bt-F1(mod)/Bt-R + 20 + + + + + 0 + 0 + 8 + 12312 + 0.41 + 0.625 + 0.78 + + + No hits found + + + 34 + Query_5 + Reverse_Primer|QL-ELE-Bt-F1(mod)/Bt-R + 20 + + + + + 0 + 0 + 8 + 12312 + 0.41 + 0.625 + 0.78 + + + No hits found + + + 35 + Query_5 + Reverse_Primer|QL-ELE-Bt-F1(mod)/Bt-R + 20 + + + + + 0 + 0 + 8 + 12312 + 0.41 + 0.625 + 0.78 + + + No hits found + + + 36 + Query_5 + Reverse_Primer|QL-ELE-Bt-F1(mod)/Bt-R + 20 + + + + + 0 + 0 + 8 + 12312 + 0.41 + 0.625 + 0.78 + + + No hits found + + + 37 + Query_5 + Reverse_Primer|QL-ELE-Bt-F1(mod)/Bt-R + 20 + + + + + 0 + 0 + 8 + 12312 + 0.41 + 0.625 + 0.78 + + + No hits found + + + 38 + Query_5 + Reverse_Primer|QL-ELE-Bt-F1(mod)/Bt-R + 20 + + + + + 0 + 0 + 8 + 12312 + 0.41 + 0.625 + 0.78 + + + No hits found + + + 39 + Query_5 + Reverse_Primer|QL-ELE-Bt-F1(mod)/Bt-R + 20 + + + + + 0 + 0 + 8 + 12312 + 0.41 + 0.625 + 0.78 + + + No hits found + + + 40 + Query_5 + Reverse_Primer|QL-ELE-Bt-F1(mod)/Bt-R + 20 + + + + + 0 + 0 + 8 + 12312 + 0.41 + 0.625 + 0.78 + + + No hits found + + + 41 + Query_6 + Probe|QL-ELE-Bt-F1(mod)/Bt-R + 25 + + + + + 0 + 0 + 9 + 16400 + 0.41 + 0.625 + 0.78 + + + No hits found + + + 42 + Query_6 + Probe|QL-ELE-Bt-F1(mod)/Bt-R + 25 + + + + + 0 + 0 + 9 + 16400 + 0.41 + 0.625 + 0.78 + + + No hits found + + + 43 + Query_6 + Probe|QL-ELE-Bt-F1(mod)/Bt-R + 25 + + + + + 0 + 0 + 9 + 16400 + 0.41 + 0.625 + 0.78 + + + No hits found + + + 44 + Query_6 + Probe|QL-ELE-Bt-F1(mod)/Bt-R + 25 + + + + + 0 + 0 + 9 + 16400 + 0.41 + 0.625 + 0.78 + + + No hits found + + + 45 + Query_6 + Probe|QL-ELE-Bt-F1(mod)/Bt-R + 25 + + + + + 0 + 0 + 9 + 16400 + 0.41 + 0.625 + 0.78 + + + No hits found + + + 46 + Query_6 + Probe|QL-ELE-Bt-F1(mod)/Bt-R + 25 + + + + + 0 + 0 + 9 + 16400 + 0.41 + 0.625 + 0.78 + + + No hits found + + + 47 + Query_6 + Probe|QL-ELE-Bt-F1(mod)/Bt-R + 25 + + + 1 + Subject_7 + AY326434|GenBank|insert_MON810|Synthetic_construct_truncated_CRYIA(b)_(cryIA(b))_gene,_partial_CDS|-2635190737607180000 + Subject_7 + 4180 + + + 1 + 37.3537 + 40 + 9.33825e-08 + 1 + 25 + 1541 + 1565 + 1 + 1 + 23 + 23 + 0 + 25 + ACATGAACAGCGCCTTGACCACAGC + ACATGAACAGCGCCCTGACCACCGC + |||||||||||||| ||||||| || + + + + + + + 0 + 0 + 9 + 16400 + 0.41 + 0.625 + 0.78 + + + + + 48 + Query_6 + Probe|QL-ELE-Bt-F1(mod)/Bt-R + 25 + + + 1 + Subject_8 + EUG|RIKILT|plasmid_pV-ZMBK07|plasmid_pV-ZMBK07|-2635190737607180000 + Subject_8 + 4983 + + + 1 + 37.3537 + 40 + 9.33825e-08 + 1 + 25 + 2344 + 2368 + 1 + 1 + 23 + 23 + 0 + 25 + ACATGAACAGCGCCTTGACCACAGC + ACATGAACAGCGCCCTGACCACCGC + |||||||||||||| ||||||| || + + + + + + + 0 + 0 + 9 + 16400 + 0.41 + 0.625 + 0.78 + + + + + 49 + Query_7 + Amplicon|QL-ELE-Bt-F1(mod)/Bt-R + 74 + + + + + 0 + 0 + 11 + 64449 + 0.41 + 0.625 + 0.78 + + + No hits found + + + 50 + Query_7 + Amplicon|QL-ELE-Bt-F1(mod)/Bt-R + 74 + + + + + 0 + 0 + 11 + 64449 + 0.41 + 0.625 + 0.78 + + + No hits found + + + 51 + Query_7 + Amplicon|QL-ELE-Bt-F1(mod)/Bt-R + 74 + + + + + 0 + 0 + 11 + 64449 + 0.41 + 0.625 + 0.78 + + + No hits found + + + 52 + Query_7 + Amplicon|QL-ELE-Bt-F1(mod)/Bt-R + 74 + + + + + 0 + 0 + 11 + 64449 + 0.41 + 0.625 + 0.78 + + + No hits found + + + 53 + Query_7 + Amplicon|QL-ELE-Bt-F1(mod)/Bt-R + 74 + + + + + 0 + 0 + 11 + 64449 + 0.41 + 0.625 + 0.78 + + + No hits found + + + 54 + Query_7 + Amplicon|QL-ELE-Bt-F1(mod)/Bt-R + 74 + + + + + 0 + 0 + 11 + 64449 + 0.41 + 0.625 + 0.78 + + + No hits found + + + 55 + Query_7 + Amplicon|QL-ELE-Bt-F1(mod)/Bt-R + 74 + + + 1 + Subject_7 + AY326434|GenBank|insert_MON810|Synthetic_construct_truncated_CRYIA(b)_(cryIA(b))_gene,_partial_CDS|-2635190737607180000 + Subject_7 + 4180 + + + 1 + 89.6514 + 98 + 6.62923e-23 + 1 + 74 + 1516 + 1589 + 1 + 1 + 64 + 64 + 0 + 74 + GAGGAAATGCGTATTCAATTCAACGACATGAACAGCGCCTTGACCACAGCTATCCCATTGTTCGCAGTCCAGAA + GAGGAGATGCGCATCCAGTTCAACGACATGAACAGCGCCCTGACCACCGCCATCCCACTCTTCGCCGTCCAGAA + ||||| ||||| || || ||||||||||||||||||||| ||||||| || |||||| | ||||| |||||||| + + + + + + + 0 + 0 + 11 + 64449 + 0.41 + 0.625 + 0.78 + + + + + 56 + Query_7 + Amplicon|QL-ELE-Bt-F1(mod)/Bt-R + 74 + + + 1 + Subject_8 + EUG|RIKILT|plasmid_pV-ZMBK07|plasmid_pV-ZMBK07|-2635190737607180000 + Subject_8 + 4983 + + + 1 + 89.6514 + 98 + 6.62923e-23 + 1 + 74 + 2319 + 2392 + 1 + 1 + 64 + 64 + 0 + 74 + GAGGAAATGCGTATTCAATTCAACGACATGAACAGCGCCTTGACCACAGCTATCCCATTGTTCGCAGTCCAGAA + GAGGAGATGCGCATCCAGTTCAACGACATGAACAGCGCCCTGACCACCGCCATCCCACTCTTCGCCGTCCAGAA + ||||| ||||| || || ||||||||||||||||||||| ||||||| || |||||| | ||||| |||||||| + + + + + + + 0 + 0 + 11 + 64449 + 0.41 + 0.625 + 0.78 + + + + + + diff -r 000000000000 -r a54279222d84 test-data/blast xml example4.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/blast xml example4.html Mon May 19 09:43:54 2014 -0400 @@ -0,0 +1,1606 @@ + + + + + + + Blast output + + + + + + + + + + +
+ +
+
This html page seems to have been stripped by Galaxy.
+ Disable Galaxy's html sanitization feature to view the full page (see sanitize_all_html in your galaxy's universe_wsgi.ini), or download this page instead of viewing it in Galaxy. +
+
+ +
+ + +
+

Queries

+ + + + + + + + + +
+ + +
+ +

Nucleotide Sequence (20 letters)

+ +
+ + + + + + + +
Query ID:Query_1
Query definition:Forward_Primer|NOST-Spec_(Genetic_ID)
Query length:20
Program:BLASTN 2.2.29+
Database:/opt/galaxy/blastdbs/EUginius_plasmid_insert
+ +
+ + +
+

Graphic Summary

+ +
+

Distribution of 7 Blast Hits on the Query Sequence

+ +
+ Mouse-over to show defline and scores, click to show alignments +
+ +
+

Color key for alignment scores

+
+
<40
+
40–50
+
50–80
+
80–200
+
200≤
+
+
+ +
+ +
+
query:
+
+
+
+
2
+
+
+
4
+
+
+
6
+
+
+
8
+
+
+
10
+
+
+
12
+
+
+
14
+
+
+
16
+
+
+
18
+
+
+
20
+
+
+
+
+
+ + +
+
+
+
+ + +
+
+
+
+ +
+
+
+
+ + + +
+

Descriptions

+ +
+

Sequences producing significant alignments:

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
DescriptionMax scoreTotal scoreQuery coverE valueIdentAccession
40.140.1100%1.513e-07100%5
40.140.1100%1.513e-07100%2
+ +
+
+ + + +
+

Alignments

+ +
+
+ + + +
+

AB209952.1|GenBank|insert_GTS-40-3-2|Glycine_max_transgenic_cp4epsps_gene_for_5-enol-pyruvylshikimate-3-phospate_synthase_class_2_precursor,_complete_cds|-9105899556052450000

+

+ Sequence ID: 5 + Length: 2457 + Number of Matches: 1 +

+
+ + +
+

+ Range 1: 2119 to 2138 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
40.1 bits(20)0.020/20(100%)0/20(0%)Plus/Plus
+ +
Query        1  AGCGCGCAAACTAGGATAAA  20
+                ||||||||||||||||||||
+Subject   2119  AGCGCGCAAACTAGGATAAA  2138
+
+ +
+ +
+ + + +
+

DJ437711|GenBank|insert_MIR604|Corn_Event_MIR604,_Left_Border_region|-5751164067366620000

+

+ Sequence ID: 2 + Length: 323 + Number of Matches: 1 +

+
+ + +
+

+ Range 1: 200 to 219 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
40.1 bits(20)0.020/20(100%)0/20(0%)Plus/Plus
+ +
Query        1  AGCGCGCAAACTAGGATAAA  20
+                ||||||||||||||||||||
+Subject    200  AGCGCGCAAACTAGGATAAA  219
+
+ +
+ +
+
+
+ +
+ +

Nucleotide Sequence (20 letters)

+ +
+ + + + + + + +
Query ID:Query_1
Query definition:Forward_Primer|NOST-Spec_(Genetic_ID)
Query length:20
Program:BLASTN 2.2.29+
Database:/opt/galaxy/blastdbs/EUginius_plasmid_insert
+ +
+ +
+

No Hits

+
+ + +
Message:No hits found
+
+
+
+ +
+ +

Nucleotide Sequence (20 letters)

+ +
+ + + + + + + +
Query ID:Query_1
Query definition:Forward_Primer|NOST-Spec_(Genetic_ID)
Query length:20
Program:BLASTN 2.2.29+
Database:/opt/galaxy/blastdbs/EUginius_plasmid_insert
+ +
+ + +
+

Graphic Summary

+ +
+

Distribution of 7 Blast Hits on the Query Sequence

+ +
+ Mouse-over to show defline and scores, click to show alignments +
+ +
+

Color key for alignment scores

+
+
<40
+
40–50
+
50–80
+
80–200
+
200≤
+
+
+ +
+ +
+
query:
+
+
+
+
2
+
+
+
4
+
+
+
6
+
+
+
8
+
+
+
10
+
+
+
12
+
+
+
14
+
+
+
16
+
+
+
18
+
+
+
20
+
+
+
+
+
+ + +
+
+
+
+ + +
+
+
+
+ + +
+
+
+
+
+ +
+
+
+
+ + + +
+

Descriptions

+ +
+

Sequences producing significant alignments:

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
DescriptionMax scoreTotal scoreQuery coverE valueIdentAccession
40.140.1100%1.513e-07100%5
40.140.1100%1.513e-07100%2
34.234.285%9.334e-06100%1
+ +
+
+ + + +
+

Alignments

+ +
+
+ + + +
+

AB209952.1|GenBank|insert_GTS-40-3-2|Glycine_max_transgenic_cp4epsps_gene_for_5-enol-pyruvylshikimate-3-phospate_synthase_class_2_precursor,_complete_cds|-9105899556052450000

+

+ Sequence ID: 5 + Length: 2457 + Number of Matches: 1 +

+
+ + +
+

+ Range 1: 2143 to 2162 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
40.1 bits(20)0.020/20(100%)0/20(0%)Plus/Plus
+ +
Query        1  CGCGCGCGGTGTCATCTATG  20
+                ||||||||||||||||||||
+Subject   2143  CGCGCGCGGTGTCATCTATG  2162
+
+ +
+ +
+ + + +
+

DJ437711|GenBank|insert_MIR604|Corn_Event_MIR604,_Left_Border_region|-5751164067366620000

+

+ Sequence ID: 2 + Length: 323 + Number of Matches: 1 +

+
+ + +
+

+ Range 1: 224 to 243 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
40.1 bits(20)0.020/20(100%)0/20(0%)Plus/Plus
+ +
Query        1  CGCGCGCGGTGTCATCTATG  20
+                ||||||||||||||||||||
+Subject    224  CGCGCGCGGTGTCATCTATG  243
+
+ +
+ +
+ + + +
+

AJ308515.1|GenBank|insert_GTS-40-3-2|Synthetic_construct_for_NOS_3'UTR/plant_junction_region.|-9105899556052450000

+

+ Sequence ID: 1 + Length: 1045 + Number of Matches: 1 +

+
+ + +
+

+ Range 1: 2 to 18 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
34.2 bits(17)0.017/17(100%)0/17(0%)Plus/Plus
+ +
Query        4  GCGCGGTGTCATCTATG  20
+                |||||||||||||||||
+Subject      2  GCGCGGTGTCATCTATG  18
+
+ +
+ +
+
+
+ +
+ +

Nucleotide Sequence (24 letters)

+ +
+ + + + + + + +
Query ID:Query_1
Query definition:Forward_Primer|NOST-Spec_(Genetic_ID)
Query length:20
Program:BLASTN 2.2.29+
Database:/opt/galaxy/blastdbs/EUginius_plasmid_insert
+ +
+ +
+

No Hits

+
+ + +
Message:No hits found
+
+
+
+ +
+ +

Nucleotide Sequence (20 letters)

+ +
+ + + + + + + +
Query ID:Query_1
Query definition:Forward_Primer|NOST-Spec_(Genetic_ID)
Query length:20
Program:BLASTN 2.2.29+
Database:/opt/galaxy/blastdbs/EUginius_plasmid_insert
+ +
+ +
+

No Hits

+
+ + +
Message:No hits found
+
+
+
+ +
+ +

Nucleotide Sequence (25 letters)

+ +
+ + + + + + + +
Query ID:Query_1
Query definition:Forward_Primer|NOST-Spec_(Genetic_ID)
Query length:20
Program:BLASTN 2.2.29+
Database:/opt/galaxy/blastdbs/EUginius_plasmid_insert
+ +
+ + +
+

Graphic Summary

+ +
+

Distribution of 7 Blast Hits on the Query Sequence

+ +
+ Mouse-over to show defline and scores, click to show alignments +
+ +
+

Color key for alignment scores

+
+
<40
+
40–50
+
50–80
+
80–200
+
200≤
+
+
+ +
+ +
+
query:
+
+
+
+
3
+
+
+
6
+
+
+
9
+
+
+
12
+
+
+
15
+
+
+
18
+
+
+
21
+
+
+
24
+
+
+
25
+
+
+
+
+
+ + +
+
+
+
+
+ + +
+
+
+
+
+ +
+
+
+
+ + + +
+

Descriptions

+ +
+

Sequences producing significant alignments:

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
DescriptionMax scoreTotal scoreQuery coverE valueIdentAccession
36.236.288%3.148e-0695%7
36.236.288%3.148e-0695%6
+ +
+
+ + + +
+

Alignments

+ +
+
+ + + +
+

EUG|RIKILT|plasmid_pV-ZMBK07|plasmid_pV-ZMBK07|-2635190737607180000

+

+ Sequence ID: 7 + Length: 4983 + Number of Matches: 1 +

+
+ + +
+

+ Range 1: 2344 to 2365 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
36.2 bits(18)0.021/22(95%)0/22(0%)Plus/Plus
+ +
Query        1  ACATGAACAGCGCCTTGACCAC  22
+                |||||||||||||| |||||||
+Subject   2344  ACATGAACAGCGCCCTGACCAC  2365
+
+ +
+ +
+ + + +
+

AY326434|GenBank|insert_MON810|Synthetic_construct_truncated_CRYIA(b)_(cryIA(b))_gene,_partial_CDS|-2635190737607180000

+

+ Sequence ID: 6 + Length: 4180 + Number of Matches: 1 +

+
+ + +
+

+ Range 1: 1541 to 1562 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
36.2 bits(18)0.021/22(95%)0/22(0%)Plus/Plus
+ +
Query        1  ACATGAACAGCGCCTTGACCAC  22
+                |||||||||||||| |||||||
+Subject   1541  ACATGAACAGCGCCCTGACCAC  1562
+
+ +
+ +
+
+
+ +
+ +

Nucleotide Sequence (74 letters)

+ +
+ + + + + + + +
Query ID:Query_1
Query definition:Forward_Primer|NOST-Spec_(Genetic_ID)
Query length:20
Program:BLASTN 2.2.29+
Database:/opt/galaxy/blastdbs/EUginius_plasmid_insert
+ +
+ + +
+

Graphic Summary

+ +
+

Distribution of 7 Blast Hits on the Query Sequence

+ +
+ Mouse-over to show defline and scores, click to show alignments +
+ +
+

Color key for alignment scores

+
+
<40
+
40–50
+
50–80
+
80–200
+
200≤
+
+
+ +
+ +
+
query:
+
+
+
+
8
+
+
+
16
+
+
+
24
+
+
+
32
+
+
+
40
+
+
+
48
+
+
+
56
+
+
+
64
+
+
+
72
+
+
+
 
+
74
+
+
+
+
+
+ + +
+
+
+
+ + +
+
+
+
+ +
+
+
+
+ + + +
+

Descriptions

+ +
+

Sequences producing significant alignments:

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
DescriptionMax scoreTotal scoreQuery coverE valueIdentAccession
67.967.9100%3.564e-1586%7
67.967.9100%3.564e-1586%6
+ +
+
+ + + +
+

Alignments

+ +
+
+ + + +
+

EUG|RIKILT|plasmid_pV-ZMBK07|plasmid_pV-ZMBK07|-2635190737607180000

+

+ Sequence ID: 7 + Length: 4983 + Number of Matches: 1 +

+
+ + +
+

+ Range 1: 2319 to 2392 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
67.9 bits(34)0.064/74(86%)0/74(0%)Plus/Plus
+ +
Query        1  GAGGAAATGCGTATTCAATTCAACGACATGAACAGCGCCTTGACCACAGCTATCCCATTGTTCGCAGTCCAGAA  74
+                ||||| ||||| || || ||||||||||||||||||||| ||||||| || |||||| | ||||| ||||||||
+Subject   2319  GAGGAGATGCGCATCCAGTTCAACGACATGAACAGCGCCCTGACCACCGCCATCCCACTCTTCGCCGTCCAGAA  2392
+
+ +
+ +
+ + + +
+

AY326434|GenBank|insert_MON810|Synthetic_construct_truncated_CRYIA(b)_(cryIA(b))_gene,_partial_CDS|-2635190737607180000

+

+ Sequence ID: 6 + Length: 4180 + Number of Matches: 1 +

+
+ + +
+

+ Range 1: 1516 to 1589 + GenBank + Graphics +

+ + + + + + + + + + + + +
ScoreExpectIdentitiesGapsStrand
67.9 bits(34)0.064/74(86%)0/74(0%)Plus/Plus
+ +
Query        1  GAGGAAATGCGTATTCAATTCAACGACATGAACAGCGCCTTGACCACAGCTATCCCATTGTTCGCAGTCCAGAA  74
+                ||||| ||||| || || ||||||||||||||||||||| ||||||| || |||||| | ||||| ||||||||
+Subject   1516  GAGGAGATGCGCATCCAGTTCAACGACATGAACAGCGCCCTGACCACCGCCATCCCACTCTTCGCCGTCCAGAA  1589
+
+ +
+ +
+
+
+ +
+ + + + + diff -r 000000000000 -r a54279222d84 test-data/blast xml example4.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/blast xml example4.xml Mon May 19 09:43:54 2014 -0400 @@ -0,0 +1,412 @@ + + + + blastn + BLASTN 2.2.29+ + Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. + /opt/galaxy/blastdbs/EUginius_plasmid_insert + Query_1 + Forward_Primer|NOST-Spec_(Genetic_ID) + 20 + + + 0.001 + 1 + -3 + 5 + 2 + L;m; + + + + + 1 + Query_1 + Forward_Primer|NOST-Spec_(Genetic_ID) + 20 + + + 1 + gnl|BL_ORD_ID|5 + AB209952.1|GenBank|insert_GTS-40-3-2|Glycine_max_transgenic_cp4epsps_gene_for_5-enol-pyruvylshikimate-3-phospate_synthase_class_2_precursor,_complete_cds|-9105899556052450000 + 5 + 2457 + + + 1 + 40.14 + 20 + 1.51296e-07 + 1 + 20 + 2119 + 2138 + 1 + 1 + 20 + 20 + 0 + 20 + AGCGCGCAAACTAGGATAAA + AGCGCGCAAACTAGGATAAA + |||||||||||||||||||| + + + + + 2 + gnl|BL_ORD_ID|2 + DJ437711|GenBank|insert_MIR604|Corn_Event_MIR604,_Left_Border_region|-5751164067366620000 + 2 + 323 + + + 1 + 40.14 + 20 + 1.51296e-07 + 1 + 20 + 200 + 219 + 1 + 1 + 20 + 20 + 0 + 20 + AGCGCGCAAACTAGGATAAA + AGCGCGCAAACTAGGATAAA + |||||||||||||||||||| + + + + + + + 8 + 15339 + 8 + 183300 + 0.710602795216363 + 1.37406312246009 + 1.30724660390929 + + + + + 2 + Query_2 + Reverse_Primer|NOST-Spec_(Genetic_ID) + 20 + + + + + 8 + 15339 + 8 + 183300 + 0.710602795216363 + 1.37406312246009 + 1.30724660390929 + + + No hits found + + + 3 + Query_3 + Probe|NOST-Spec_(Genetic_ID) + 20 + + + 1 + gnl|BL_ORD_ID|5 + AB209952.1|GenBank|insert_GTS-40-3-2|Glycine_max_transgenic_cp4epsps_gene_for_5-enol-pyruvylshikimate-3-phospate_synthase_class_2_precursor,_complete_cds|-9105899556052450000 + 5 + 2457 + + + 1 + 40.14 + 20 + 1.51296e-07 + 1 + 20 + 2143 + 2162 + 1 + 1 + 20 + 20 + 0 + 20 + CGCGCGCGGTGTCATCTATG + CGCGCGCGGTGTCATCTATG + |||||||||||||||||||| + + + + + 2 + gnl|BL_ORD_ID|2 + DJ437711|GenBank|insert_MIR604|Corn_Event_MIR604,_Left_Border_region|-5751164067366620000 + 2 + 323 + + + 1 + 40.14 + 20 + 1.51296e-07 + 1 + 20 + 224 + 243 + 1 + 1 + 20 + 20 + 0 + 20 + CGCGCGCGGTGTCATCTATG + CGCGCGCGGTGTCATCTATG + |||||||||||||||||||| + + + + + 3 + gnl|BL_ORD_ID|1 + AJ308515.1|GenBank|insert_GTS-40-3-2|Synthetic_construct_for_NOS_3'UTR/plant_junction_region.|-9105899556052450000 + 1 + 1045 + + + 1 + 34.1929 + 17 + 9.33411e-06 + 4 + 20 + 2 + 18 + 1 + 1 + 17 + 17 + 0 + 17 + GCGCGGTGTCATCTATG + GCGCGGTGTCATCTATG + ||||||||||||||||| + + + + + + + 8 + 15339 + 8 + 183300 + 0.710602795216363 + 1.37406312246009 + 1.30724660390929 + + + + + 4 + Query_4 + Forward_Primer|QL-ELE-Bt-F1(mod)/Bt-R + 24 + + + + + 8 + 15339 + 9 + 229005 + 0.710602795216363 + 1.37406312246009 + 1.30724660390929 + + + No hits found + + + 5 + Query_5 + Reverse_Primer|QL-ELE-Bt-F1(mod)/Bt-R + 20 + + + + + 8 + 15339 + 8 + 183300 + 0.710602795216363 + 1.37406312246009 + 1.30724660390929 + + + No hits found + + + 6 + Query_6 + Probe|QL-ELE-Bt-F1(mod)/Bt-R + 25 + + + 1 + gnl|BL_ORD_ID|7 + EUG|RIKILT|plasmid_pV-ZMBK07|plasmid_pV-ZMBK07|-2635190737607180000 + 7 + 4983 + + + 1 + 36.1753 + 18 + 3.14801e-06 + 1 + 22 + 2344 + 2365 + 1 + 1 + 21 + 21 + 0 + 22 + ACATGAACAGCGCCTTGACCAC + ACATGAACAGCGCCCTGACCAC + |||||||||||||| ||||||| + + + + + 2 + gnl|BL_ORD_ID|6 + AY326434|GenBank|insert_MON810|Synthetic_construct_truncated_CRYIA(b)_(cryIA(b))_gene,_partial_CDS|-2635190737607180000 + 6 + 4180 + + + 1 + 36.1753 + 18 + 3.14801e-06 + 1 + 22 + 1541 + 1562 + 1 + 1 + 21 + 21 + 0 + 22 + ACATGAACAGCGCCTTGACCAC + ACATGAACAGCGCCCTGACCAC + |||||||||||||| ||||||| + + + + + + + 8 + 15339 + 9 + 244272 + 0.710602795216363 + 1.37406312246009 + 1.30724660390929 + + + + + 7 + Query_7 + Amplicon|QL-ELE-Bt-F1(mod)/Bt-R + 74 + + + 1 + gnl|BL_ORD_ID|7 + EUG|RIKILT|plasmid_pV-ZMBK07|plasmid_pV-ZMBK07|-2635190737607180000 + 7 + 4983 + + + 1 + 67.8929 + 34 + 3.56369e-15 + 1 + 74 + 2319 + 2392 + 1 + 1 + 64 + 64 + 0 + 74 + GAGGAAATGCGTATTCAATTCAACGACATGAACAGCGCCTTGACCACAGCTATCCCATTGTTCGCAGTCCAGAA + GAGGAGATGCGCATCCAGTTCAACGACATGAACAGCGCCCTGACCACCGCCATCCCACTCTTCGCCGTCCAGAA + ||||| ||||| || || ||||||||||||||||||||| ||||||| || |||||| | ||||| |||||||| + + + + + 2 + gnl|BL_ORD_ID|6 + AY326434|GenBank|insert_MON810|Synthetic_construct_truncated_CRYIA(b)_(cryIA(b))_gene,_partial_CDS|-2635190737607180000 + 6 + 4180 + + + 1 + 67.8929 + 34 + 3.56369e-15 + 1 + 74 + 1516 + 1589 + 1 + 1 + 64 + 64 + 0 + 74 + GAGGAAATGCGTATTCAATTCAACGACATGAACAGCGCCTTGACCACAGCTATCCCATTGTTCGCAGTCCAGAA + GAGGAGATGCGCATCCAGTTCAACGACATGAACAGCGCCCTGACCACCGCCATCCCACTCTTCGCCGTCCAGAA + ||||| ||||| || || ||||||||||||||||||||| ||||||| || |||||| | ||||| |||||||| + + + + + + + 8 + 15339 + 10 + 976576 + 0.710602795216363 + 1.37406312246009 + 1.30724660390929 + + + + + + diff -r 000000000000 -r a54279222d84 test-data/refresh_test_results.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/refresh_test_results.sh Mon May 19 09:43:54 2014 -0400 @@ -0,0 +1,8 @@ +#!/bin/sh + +# run this from the directory it exists in to update the test outputs + +for i in 1 2 3 4 +do + ../blast2html.py -i "blast xml example$i.xml" -o "blast xml example$i.html" +done