# HG changeset patch # User yhoogstrate # Date 1462527936 14400 # Node ID 487f438da0990b70aa85ff4404e723941366064e # Parent 312edff152ebf7dcf416897e468edc89e5e7a549 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 879dad538d7c2fa8b7e7f3e9460ff88874797d2c diff -r 312edff152eb -r 487f438da099 energy-estimation-utility.xml --- a/energy-estimation-utility.xml Thu Mar 31 04:20:55 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,111 +0,0 @@ - - Estimate the maximal energy a segment needs to assign to become part of the optimal structure using segmentation-fold - - - segmentation-fold - python - - - - - segmentation-fold --version | head -n 2 | tail -n 1 | sed -e 's/^[[:space:]]*//' -e 's/[[:space:]]*$//' - - "${output_list}" - ]]> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @mastersthesis{mastersthesis, - author = {Youri Hoogstrate}, - title = {An algorithm for predicting RNA 2D structures including K-turns}, - school = {University of Technology Delft, Leiden University}, - year = 2012, - address = {}, - month = 11, - note = {Research assignment for Master Computer-science}, - url = { https://yh-kt-fold.googlecode.com/files/Report.pdf } - } - - - diff -r 312edff152eb -r 487f438da099 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Fri May 06 05:45:36 2016 -0400 @@ -0,0 +1,41 @@ + + smf-v1.6-4_utils-v1.0.3 + + + + + + + + + segmentation-fold --version | head -n 2 | tail -n 1 | sed -e 's/^[[:space:]]*//' -e 's/[[:space:]]*$//' + segmentation-fold-utils --version + + + segmentation-fold-utils + python + ]]> + + segmentation-fold + ]]> + + + + + + @mastersthesis{mastersthesis, + author = {Youri Hoogstrate}, + title = {An algorithm for predicting RNA 2D structures including K-turns}, + school = {University of Technology Delft, Leiden University}, + year = 2012, + address = {}, + month = 11, + note = {Research assignment for Master Computer-science}, + url = { https://yh-kt-fold.googlecode.com/files/Report.pdf } + } + + + + diff -r 312edff152eb -r 487f438da099 scan-for-segments.xml --- a/scan-for-segments.xml Thu Mar 31 04:20:55 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,105 +0,0 @@ - - Scan for the presence of segments in sequences using segmentation-fold - - - segmentation-fold - python - - - - - segmentation-fold --version | head -n 2 | tail -n 1 | sed -e 's/^[[:space:]]*//' -e 's/[[:space:]]*$//' - - $output_list - ]]> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @mastersthesis{mastersthesis, - author = {Youri Hoogstrate}, - title = {An algorithm for predicting RNA 2D structures including K-turns}, - school = {University of Technology Delft, Leiden University}, - year = 2012, - address = {}, - month = 11, - note = {Research assignment for Master Computer-science}, - url = { https://yh-kt-fold.googlecode.com/files/Report.pdf } - } - - - diff -r 312edff152eb -r 487f438da099 segmentation-fold.xml --- a/segmentation-fold.xml Thu Mar 31 04:20:55 2016 -0400 +++ b/segmentation-fold.xml Fri May 06 05:45:36 2016 -0400 @@ -1,13 +1,15 @@ - + RNA-Folding including predefined segments including K-turns + + macros.xml + - segmentation-fold + @VERSION_COMMAND_SMF@ + - - - segmentation-fold --version | head -n 2 | tail -n 1 | sed -e 's/^[[:space:]]*//' -e 's/[[:space:]]*$//' + @VERSION_COMMAND_SMF@ - - - @mastersthesis{mastersthesis, - author = {Youri Hoogstrate}, - title = {An algorithm for predicting RNA 2D structures including K-turns}, - school = {University of Technology Delft, Leiden University}, - year = 2012, - address = {}, - month = 11, - note = {Research assignment for Master Computer-science}, - url = { https://yh-kt-fold.googlecode.com/files/Report.pdf } - } - - + diff -r 312edff152eb -r 487f438da099 test-data/DBNFile.test_01.in.bam Binary file test-data/DBNFile.test_01.in.bam has changed diff -r 312edff152eb -r 487f438da099 test-data/DBNFile.test_01.in.dbn --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/DBNFile.test_01.in.dbn Fri May 06 05:45:36 2016 -0400 @@ -0,0 +1,8 @@ +>chr1:10-21 x unknown-01 +GGGGAAACCCC +((((...)))) ((.((.)).)) -2.5 +((.((.)).)) (((((.))))) -3.5 +>chr1:25-36 x unknown-01 +AAAAAAAAAAA +>chr1:45-56 x unknown-01 +AAAAAAAAAAA diff -r 312edff152eb -r 487f438da099 test-data/DBNFile.test_02.in.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/DBNFile.test_02.in.bed Fri May 06 05:45:36 2016 -0400 @@ -0,0 +1,6 @@ +chr1 0 1 firstbase 0 + +chr1 0 5 1-2-3-4-5 0 + +chr1 5 10 6-7-8-9-10 0 + +chr1 10 11 hideme 0 + +chr2 0 5 hideme2 0 + +chr2 5 10 hideme3 0 + diff -r 312edff152eb -r 487f438da099 test-data/DBNFile.test_02.in.dbn --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/DBNFile.test_02.in.dbn Fri May 06 05:45:36 2016 -0400 @@ -0,0 +1,6 @@ +>chr1:0-10 x unknown-01 +AAAAAAAAAA +>chr1:25-36 x unknown-01 (aligned reads tests/test-data/DBNFile.test_01.in.bam: 1) +AAAAAAAAAAA +>chr1:45-56 x unknown-01 (aligned reads tests/test-data/DBNFile.test_01.in.bam: 2) +AAAAAAAAAAA diff -r 312edff152eb -r 487f438da099 test-data/DBNFile.test_02.out.n.dbn --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/DBNFile.test_02.out.n.dbn Fri May 06 05:45:36 2016 -0400 @@ -0,0 +1,4 @@ +>chr1:25-36 x unknown-01 (aligned reads tests/test-data/DBNFile.test_01.in.bam: 1) +AAAAAAAAAAA +>chr1:45-56 x unknown-01 (aligned reads tests/test-data/DBNFile.test_01.in.bam: 2) +AAAAAAAAAAA diff -r 312edff152eb -r 487f438da099 test-data/DBNFile.test_02.out.o.dbn --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/DBNFile.test_02.out.o.dbn Fri May 06 05:45:36 2016 -0400 @@ -0,0 +1,2 @@ +>chr1:0-10 x unknown-01 (overlap in tests/test-data/DBNFile.test_02.in.bed: firstbase,1-2-3-4-5,6-7-8-9-10) +AAAAAAAAAA diff -r 312edff152eb -r 487f438da099 test-data/ExtractBoxedSequences.test_01.in.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ExtractBoxedSequences.test_01.in.bed Fri May 06 05:45:36 2016 -0400 @@ -0,0 +1,6 @@ +chr10 0 7 box1-f:NRTGATG 0 + +chr10 14 18 box2-f:CTGA 0 + +chr10 28 35 box1-f:NRTGATG 0 + +chr10 42 46 box2-f:CTGA 0 + +chr10 56 63 box1-f:NRTGATG 0 + +chr10 70 74 box2-f:CTGA 0 + diff -r 312edff152eb -r 487f438da099 test-data/ExtractBoxedSequences.test_01.in.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ExtractBoxedSequences.test_01.in.fa Fri May 06 05:45:36 2016 -0400 @@ -0,0 +1,12 @@ +>chr10 +AATGATG +aaaaaaa +CTGAaaa +ccccccc +AATGATG +aaaaaaa +CTGAaaa +ccccccc +AATGATG +aaaaaaa +CTGAaaa diff -r 312edff152eb -r 487f438da099 test-data/ExtractBoxedSequences.test_01.out.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ExtractBoxedSequences.test_01.out.fa Fri May 06 05:45:36 2016 -0400 @@ -0,0 +1,12 @@ +>chr10:0-18(+) +AATGATGaaaaaaaCTGA +>chr10:0-46(+) +AATGATGaaaaaaaCTGAaaacccccccAATGATGaaaaaaaCTGA +>chr10:0-74(+) +AATGATGaaaaaaaCTGAaaacccccccAATGATGaaaaaaaCTGAaaacccccccAATGATGaaaaaaaCTGA +>chr10:28-46(+) +AATGATGaaaaaaaCTGA +>chr10:28-74(+) +AATGATGaaaaaaaCTGAaaacccccccAATGATGaaaaaaaCTGA +>chr10:56-74(+) +AATGATGaaaaaaaCTGA diff -r 312edff152eb -r 487f438da099 test-data/FindBoxes.genome.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/FindBoxes.genome.fa Fri May 06 05:45:36 2016 -0400 @@ -0,0 +1,44 @@ +>chr1 +aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa +>chr2 +aaaaaCTGAaaaaaaaCTGAaaaaa +>chr3 +CTGAaaaaaaaCTGA +>chr4 +CTGACTGA +>chr5 +TCAGaaaaaaTCAG +>chr6 +tcagAAAAAAtcag +>chr7 +AATGATG +CATGATG +TATGATG +GATGATG +AGTGATG +CGTGATG +TGTGATG +GGTGATG +>chr8_no_valid_C_boxes +ACTGATG +CCTGATG +TCTGATG +GCTGATG +ATTGATG +CTTGATG +TTTGATG +GTTGATG +>chr9 +CATCACCCATCACACATCACGCATCACTCATCATCCATCATACATCATGCATCATT +>chr10 +AATGATG +aaaaaaa +CTGAaaa +ccccccc +AATGATG +aaaaaaa +CTGAaaa +ccccccc +AATGATG +aaaaaaa +CTGAaaa diff -r 312edff152eb -r 487f438da099 test-data/FindBoxes.test_02.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/FindBoxes.test_02.bed Fri May 06 05:45:36 2016 -0400 @@ -0,0 +1,36 @@ +chr2 5 9 box2-f:CTGA 0 + +chr2 16 20 box2-f:CTGA 0 + +chr3 0 4 box2-f:CTGA 0 + +chr3 11 15 box2-f:CTGA 0 + +chr4 0 4 box2-f:CTGA 0 + +chr4 4 8 box2-f:CTGA 0 + +chr5 0 4 box2-r:TCAG 0 - +chr5 10 14 box2-r:TCAG 0 - +chr6 0 4 box2-r:TCAG 0 - +chr6 10 14 box2-r:TCAG 0 - +chr7 0 7 box1-f:NRTGATG 0 + +chr7 7 14 box1-f:NRTGATG 0 + +chr7 14 21 box1-f:NRTGATG 0 + +chr7 21 28 box1-f:NRTGATG 0 + +chr7 28 35 box1-f:NRTGATG 0 + +chr7 35 42 box1-f:NRTGATG 0 + +chr7 42 49 box1-f:NRTGATG 0 + +chr7 49 56 box1-f:NRTGATG 0 + +chr8_no_valid_C_boxes 1 5 box2-f:CTGA 0 + +chr8_no_valid_C_boxes 8 12 box2-f:CTGA 0 + +chr8_no_valid_C_boxes 15 19 box2-f:CTGA 0 + +chr8_no_valid_C_boxes 22 26 box2-f:CTGA 0 + +chr9 0 7 box1-r:CATCAYN 0 - +chr9 7 14 box1-r:CATCAYN 0 - +chr9 14 21 box1-r:CATCAYN 0 - +chr9 21 28 box1-r:CATCAYN 0 - +chr9 28 35 box1-r:CATCAYN 0 - +chr9 35 42 box1-r:CATCAYN 0 - +chr9 42 49 box1-r:CATCAYN 0 - +chr9 49 56 box1-r:CATCAYN 0 - +chr10 0 7 box1-f:NRTGATG 0 + +chr10 14 18 box2-f:CTGA 0 + +chr10 28 35 box1-f:NRTGATG 0 + +chr10 42 46 box2-f:CTGA 0 + +chr10 56 63 box1-f:NRTGATG 0 + +chr10 70 74 box2-f:CTGA 0 + diff -r 312edff152eb -r 487f438da099 test-data/SNORD114-4-revised.scan-for-segments.txt --- a/test-data/SNORD114-4-revised.scan-for-segments.txt Thu Mar 31 04:20:55 2016 -0400 +++ b/test-data/SNORD114-4-revised.scan-for-segments.txt Fri May 06 05:45:36 2016 -0400 @@ -1,74 +1,57 @@ ->SNORD114-4 x Kt-42.dra -CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA ->SNORD114-4 x Kt-42.eco +>SNORD114-4 revised x Kt-7 G2nA SAM riboswitch H. marismortui CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA ->SNORD114-4 x Loop-E-Motif.bac +>SNORD114-4 revised x Kt-7 T. thermophilus CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA ->SNORD114-4 x Kt-CD-box.UAU +>SNORD114-4 revised x Kt-7 E. coli CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA ->SNORD114-4 x Kt-CD-box.UGU +>SNORD114-4 revised x Kt-7 D. radiodurans CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA ->SNORD114-4 x Kt-CD-box.CAU +>SNORD114-4 revised x Kt-11 T. thermophilus CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA ->SNORD114-4 x Kt-42.tth +>SNORD114-4 revised x Kt-11.eco CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA ->SNORD114-4 x Kt-G2nA-SAM-riboswitch (T. tengcongensi) -CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA ->SNORD114-4 x Kt-7 G2nA SAM riboswitch (H. marismortui) +>SNORD114-4 revised x Kt-15.hma CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA ->SNORD114-4 x Kt-15.hma +.(((((((((.......)))))).((.((((..((..((((((..........)))))).))..))))..))))) .((((((....(((.((.....((((......))))((....))...)...))))...(((....))).)))))) -6.42471313477 +>SNORD114-4 revised x Kt-23.tth CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA -.(((((((((.......)))))).((.((((..((..((((((..........)))))).))..))))..))))) .((((((....(((.((.....((((......))))((....))...)...))))...(((....))).)))))) -6.4197063446 ->SNORD114-4 x Kt-U4b.hsa +>SNORD114-4 revised x Kt-23.eco CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA ->SNORD114-4 x Kt-CD-box.GGU -CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA ->SNORD114-4 x Kt-7 (E. coli) +>SNORD114-4 revised x Kt-38.hma CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA ->SNORD114-4 x Kt-7 (D. radiodurans) +>SNORD114-4 revised x Kt-42.hma CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA ->SNORD114-4 x Kt-58.hma +>SNORD114-4 revised x Kt-42.tth CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA ->SNORD114-4 x Kt-46.tth +>SNORD114-4 revised x Kt-42.dra CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA ->SNORD114-4 x Kt-SAM-ribo.tte -CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA ->SNORD114-4 x Kt-23.eco +>SNORD114-4 revised x Kt-42.eco CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA ->SNORD114-4 x Kt-38.hma -CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA ->SNORD114-4 x Kt-46.dra +>SNORD114-4 revised x Kt-46.hma CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA ->SNORD114-4 x Kt-CD-box.CGU +>SNORD114-4 revised x Kt-46.tth CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA ->SNORD114-4 x Kt-T-box.bsu +>SNORD114-4 revised x Kt-46.dra CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA ->SNORD114-4 x Kt-23.tth +>SNORD114-4 revised x Kt-46.eco CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA ->SNORD114-4 x Kt-46.eco +>SNORD114-4 revised x Kt-58.hma CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA ->SNORD114-4 x Kt-c-di-GMP-II.cac +>SNORD114-4 revised x Kt-U4a.hsa CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA ->SNORD114-4 x Kt-11 (T. thermophilus) -CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA ->SNORD114-4 x Kt-CD-box.AAU +>SNORD114-4 revised x Kt-U4b.hsa CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA ->SNORD114-4 x Kt-L30e.sce -CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA ->SNORD114-4 x Kt-7 (T. thermophilus) +>SNORD114-4 revised x Kt-CD-box.CGU CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA ->SNORD114-4 x Kt-42.hma +>SNORD114-4 revised x Kt-CD-box.UGU CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA ->SNORD114-4 x Kt-U4a.hsa -CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA ->SNORD114-4 x Kt-G2nA-SAMribo.bsu +>SNORD114-4 revised x Kt-L30e.sce CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA ->SNORD114-4 x Kt-CD-box.GAU +>SNORD114-4 revised x Kt-SAM-ribo.tte CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA ->SNORD114-4 x Kt-11.eco +>SNORD114-4 revised x Kt-T-box.bsu CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA ->SNORD114-4 x Kt-46.hma +>SNORD114-4 revised x Kt-c-di-GMP-II.cac CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA ->SNORD114-4 x Kt-CD-box.AGU +>SNORD114-4 revised x Kt-G2nA-SAM-riboswitch T. tengcongensi CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA -.(((((((((.......)))))).((.((((..((..((((((..........)))))).))..))))..))))) .((((((...(((((.......((((......)))).((((((..........)))))).....))))))))))) 1.99971199036 diff -r 312edff152eb -r 487f438da099 test-data/SNORD118-revised.scan-for-segments.txt --- a/test-data/SNORD118-revised.scan-for-segments.txt Thu Mar 31 04:20:55 2016 -0400 +++ b/test-data/SNORD118-revised.scan-for-segments.txt Fri May 06 05:45:36 2016 -0400 @@ -1,75 +1,57 @@ ->SNORD118 x Kt-42.dra -AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC ->SNORD118 x Kt-42.eco +>SNORD118 revised x Kt-7 G2nA SAM riboswitch H. marismortui AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC ->SNORD118 x Loop-E-Motif.bac +>SNORD118 revised x Kt-7 T. thermophilus AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC ->SNORD118 x Kt-CD-box.UAU +>SNORD118 revised x Kt-7 E. coli AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC ->SNORD118 x Kt-CD-box.UGU +>SNORD118 revised x Kt-7 D. radiodurans AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC ->SNORD118 x Kt-CD-box.CAU +>SNORD118 revised x Kt-11 T. thermophilus AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC -.(((.((.(.(((.(((((((((.((.((((.....)))).)))))))(((((((...........))))))).)))).)))).))))) .(((...((((((.(((((((((.((.((((.....)))).)))))))(((((((...........))))))).)))).))))))))). 3.380651474 ->SNORD118 x Kt-42.tth +>SNORD118 revised x Kt-11.eco AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC ->SNORD118 x Kt-G2nA-SAM-riboswitch (T. tengcongensi) +>SNORD118 revised x Kt-15.hma AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC ->SNORD118 x Kt-7 G2nA SAM riboswitch (H. marismortui) -AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC ->SNORD118 x Kt-15.hma +>SNORD118 revised x Kt-23.tth AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC ->SNORD118 x Kt-U4b.hsa +>SNORD118 revised x Kt-23.eco AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC ->SNORD118 x Kt-CD-box.GGU -AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC ->SNORD118 x Kt-7 (E. coli) +>SNORD118 revised x Kt-38.hma AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC ->SNORD118 x Kt-7 (D. radiodurans) +>SNORD118 revised x Kt-42.hma AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC ->SNORD118 x Kt-58.hma +>SNORD118 revised x Kt-42.tth AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC ->SNORD118 x Kt-46.tth +>SNORD118 revised x Kt-42.dra AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC ->SNORD118 x Kt-SAM-ribo.tte -AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC ->SNORD118 x Kt-23.eco +>SNORD118 revised x Kt-42.eco AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC ->SNORD118 x Kt-38.hma -AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC ->SNORD118 x Kt-46.dra +>SNORD118 revised x Kt-46.hma AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC ->SNORD118 x Kt-CD-box.CGU +>SNORD118 revised x Kt-46.tth AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC -.(((.((.(.(((.(((((((((.((.((((.....)))).)))))))(((((((...........))))))).)))).)))).))))) (((((...((((((............))...))))...))......(((((((((...........))))))))).....)))...... -15.021024704 ->SNORD118 x Kt-T-box.bsu +>SNORD118 revised x Kt-46.dra AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC ->SNORD118 x Kt-23.tth +>SNORD118 revised x Kt-46.eco AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC ->SNORD118 x Kt-46.eco +>SNORD118 revised x Kt-58.hma AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC ->SNORD118 x Kt-c-di-GMP-II.cac +>SNORD118 revised x Kt-U4a.hsa AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC ->SNORD118 x Kt-11 (T. thermophilus) -AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC ->SNORD118 x Kt-CD-box.AAU +>SNORD118 revised x Kt-U4b.hsa AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC ->SNORD118 x Kt-L30e.sce -AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC ->SNORD118 x Kt-7 (T. thermophilus) +>SNORD118 revised x Kt-CD-box.CGU AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC ->SNORD118 x Kt-42.hma +.(((.((.(.(((.(((((((((.((.((((.....)))).)))))))(((((((...........))))))).)))).)))).))))) (((((...((((((............))...))))...))......(((((((((...........))))))))).....)))...... -15.038848877 +>SNORD118 revised x Kt-CD-box.UGU AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC ->SNORD118 x Kt-U4a.hsa -AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC ->SNORD118 x Kt-G2nA-SAMribo.bsu +>SNORD118 revised x Kt-L30e.sce AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC ->SNORD118 x Kt-CD-box.GAU +>SNORD118 revised x Kt-SAM-ribo.tte AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC -.(((.((.(.(((.(((((((((.((.((((.....)))).)))))))(((((((...........))))))).)))).)))).))))) (((.(((...(((((......))))))((((.....))))...)).(((((((((...........))))))))).....)))...... -8.30012321472 ->SNORD118 x Kt-11.eco +>SNORD118 revised x Kt-T-box.bsu AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC ->SNORD118 x Kt-46.hma +>SNORD118 revised x Kt-c-di-GMP-II.cac AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC ->SNORD118 x Kt-CD-box.AGU +>SNORD118 revised x Kt-G2nA-SAM-riboswitch T. tengcongensi AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC diff -r 312edff152eb -r 487f438da099 test-data/SNORD13-revised.scan-for-segments.txt --- a/test-data/SNORD13-revised.scan-for-segments.txt Thu Mar 31 04:20:55 2016 -0400 +++ b/test-data/SNORD13-revised.scan-for-segments.txt Fri May 06 05:45:36 2016 -0400 @@ -1,74 +1,57 @@ ->SNORD13 x Kt-42.dra -GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC ->SNORD13 x Kt-42.eco +>SNORD13 revised x Kt-7 G2nA SAM riboswitch H. marismortui GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC ->SNORD13 x Loop-E-Motif.bac +>SNORD13 revised x Kt-7 T. thermophilus GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC ->SNORD13 x Kt-CD-box.UAU +>SNORD13 revised x Kt-7 E. coli GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC ->SNORD13 x Kt-CD-box.UGU +>SNORD13 revised x Kt-7 D. radiodurans GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC ->SNORD13 x Kt-CD-box.CAU +>SNORD13 revised x Kt-11 T. thermophilus GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC ->SNORD13 x Kt-42.tth +>SNORD13 revised x Kt-11.eco GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC ->SNORD13 x Kt-G2nA-SAM-riboswitch (T. tengcongensi) -GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC ->SNORD13 x Kt-7 G2nA SAM riboswitch (H. marismortui) +>SNORD13 revised x Kt-15.hma GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC ->SNORD13 x Kt-15.hma -GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC ->SNORD13 x Kt-U4b.hsa +>SNORD13 revised x Kt-23.tth GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC ->SNORD13 x Kt-CD-box.GGU +>SNORD13 revised x Kt-23.eco GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC ->SNORD13 x Kt-7 (E. coli) +>SNORD13 revised x Kt-38.hma GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC ->SNORD13 x Kt-7 (D. radiodurans) +>SNORD13 revised x Kt-42.hma GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC ->SNORD13 x Kt-58.hma +>SNORD13 revised x Kt-42.tth GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC ->SNORD13 x Kt-46.tth +>SNORD13 revised x Kt-42.dra GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC ->SNORD13 x Kt-SAM-ribo.tte -GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC ->SNORD13 x Kt-23.eco +>SNORD13 revised x Kt-42.eco GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC ->SNORD13 x Kt-38.hma -GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC ->SNORD13 x Kt-46.dra +>SNORD13 revised x Kt-46.hma GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC ->SNORD13 x Kt-CD-box.CGU +>SNORD13 revised x Kt-46.tth GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC -(((((.(..((.(((....((((((((((((....)))))))(((((((..(.((((((...))).))).)..)))))))))))))))))..)))))) (((((.(.(...((((((.((((((((((((....)))))))(((((((..(.((((((...))).))).)..))))))))))))))))))))))))) 3.35026359558 ->SNORD13 x Kt-T-box.bsu +>SNORD13 revised x Kt-46.dra GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC ->SNORD13 x Kt-23.tth +>SNORD13 revised x Kt-46.eco GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC ->SNORD13 x Kt-46.eco +>SNORD13 revised x Kt-58.hma GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC ->SNORD13 x Kt-c-di-GMP-II.cac +>SNORD13 revised x Kt-U4a.hsa GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC ->SNORD13 x Kt-11 (T. thermophilus) -GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC ->SNORD13 x Kt-CD-box.AAU +>SNORD13 revised x Kt-U4b.hsa GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC ->SNORD13 x Kt-L30e.sce -GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC ->SNORD13 x Kt-7 (T. thermophilus) +>SNORD13 revised x Kt-CD-box.CGU GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC ->SNORD13 x Kt-42.hma +(((((.(..((.(((....((((((((((((....)))))))(((((((..(.((((((...))).))).)..)))))))))))))))))..)))))) (((((.(.(...((((((.((((((((((((....)))))))(((((((..(.((((((...))).))).)..))))))))))))))))))))))))) 3.37054443359 +>SNORD13 revised x Kt-CD-box.UGU GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC ->SNORD13 x Kt-U4a.hsa -GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC ->SNORD13 x Kt-G2nA-SAMribo.bsu +>SNORD13 revised x Kt-L30e.sce GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC ->SNORD13 x Kt-CD-box.GAU +>SNORD13 revised x Kt-SAM-ribo.tte GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC -(((((.(..((.(((....((((((((((((....)))))))(((((((..(.((((((...))).))).)..)))))))))))))))))..)))))) (((((((.((((...((((((((((....))))))..)))))...)))))............((((.((((.((........)))))))))).))))) -9.91994667053 ->SNORD13 x Kt-11.eco +>SNORD13 revised x Kt-T-box.bsu GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC ->SNORD13 x Kt-46.hma +>SNORD13 revised x Kt-c-di-GMP-II.cac GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC ->SNORD13 x Kt-CD-box.AGU +>SNORD13 revised x Kt-G2nA-SAM-riboswitch T. tengcongensi GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC diff -r 312edff152eb -r 487f438da099 test-data/SNORD48-revised.scan-for-segments.txt --- a/test-data/SNORD48-revised.scan-for-segments.txt Thu Mar 31 04:20:55 2016 -0400 +++ b/test-data/SNORD48-revised.scan-for-segments.txt Fri May 06 05:45:36 2016 -0400 @@ -1,74 +1,56 @@ ->SNORD48 x Kt-42.dra -GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC ->SNORD48 x Kt-42.eco +>SNORD48 revised 2 extra bases on 5 end x Kt-7 G2nA SAM riboswitch H. marismortui GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC ->SNORD48 x Loop-E-Motif.bac +>SNORD48 revised 2 extra bases on 5 end x Kt-7 T. thermophilus GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC ->SNORD48 x Kt-CD-box.UAU +>SNORD48 revised 2 extra bases on 5 end x Kt-7 E. coli GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC ->SNORD48 x Kt-CD-box.UGU +>SNORD48 revised 2 extra bases on 5 end x Kt-7 D. radiodurans GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC ->SNORD48 x Kt-CD-box.CAU +>SNORD48 revised 2 extra bases on 5 end x Kt-11 T. thermophilus GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC ->SNORD48 x Kt-42.tth +>SNORD48 revised 2 extra bases on 5 end x Kt-11.eco GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC ->SNORD48 x Kt-G2nA-SAM-riboswitch (T. tengcongensi) -GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC ->SNORD48 x Kt-7 G2nA SAM riboswitch (H. marismortui) +>SNORD48 revised 2 extra bases on 5 end x Kt-15.hma GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC ->SNORD48 x Kt-15.hma -GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC ->SNORD48 x Kt-U4b.hsa +>SNORD48 revised 2 extra bases on 5 end x Kt-23.tth GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC ->SNORD48 x Kt-CD-box.GGU +>SNORD48 revised 2 extra bases on 5 end x Kt-23.eco GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC ->SNORD48 x Kt-7 (E. coli) +>SNORD48 revised 2 extra bases on 5 end x Kt-38.hma GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC ->SNORD48 x Kt-7 (D. radiodurans) +>SNORD48 revised 2 extra bases on 5 end x Kt-42.hma GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC ->SNORD48 x Kt-58.hma +>SNORD48 revised 2 extra bases on 5 end x Kt-42.tth GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC ->SNORD48 x Kt-46.tth +>SNORD48 revised 2 extra bases on 5 end x Kt-42.dra GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC ->SNORD48 x Kt-SAM-ribo.tte -GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC ->SNORD48 x Kt-23.eco +>SNORD48 revised 2 extra bases on 5 end x Kt-42.eco GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC ->SNORD48 x Kt-38.hma -GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC ->SNORD48 x Kt-46.dra +>SNORD48 revised 2 extra bases on 5 end x Kt-46.hma GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC ->SNORD48 x Kt-CD-box.CGU +>SNORD48 revised 2 extra bases on 5 end x Kt-46.tth GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC ->SNORD48 x Kt-T-box.bsu +>SNORD48 revised 2 extra bases on 5 end x Kt-46.dra GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC ->SNORD48 x Kt-23.tth +>SNORD48 revised 2 extra bases on 5 end x Kt-46.eco GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC ->SNORD48 x Kt-46.eco +>SNORD48 revised 2 extra bases on 5 end x Kt-58.hma GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC ->SNORD48 x Kt-c-di-GMP-II.cac +>SNORD48 revised 2 extra bases on 5 end x Kt-U4a.hsa GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC ->SNORD48 x Kt-11 (T. thermophilus) -GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC ->SNORD48 x Kt-CD-box.AAU +>SNORD48 revised 2 extra bases on 5 end x Kt-U4b.hsa GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC ->SNORD48 x Kt-L30e.sce -GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC ->SNORD48 x Kt-7 (T. thermophilus) +>SNORD48 revised 2 extra bases on 5 end x Kt-CD-box.CGU GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC ->SNORD48 x Kt-42.hma +>SNORD48 revised 2 extra bases on 5 end x Kt-CD-box.UGU GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC ->SNORD48 x Kt-U4a.hsa -GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC ->SNORD48 x Kt-G2nA-SAMribo.bsu +>SNORD48 revised 2 extra bases on 5 end x Kt-L30e.sce GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC ->SNORD48 x Kt-CD-box.GAU +>SNORD48 revised 2 extra bases on 5 end x Kt-SAM-ribo.tte GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC -((((((.((.((((((((((.....)))).).).)))).((((...))))...)).)))))).... (((((...(((((((...))).....))))).....(((((............))))))))).... -10.9206504822 ->SNORD48 x Kt-11.eco +>SNORD48 revised 2 extra bases on 5 end x Kt-T-box.bsu GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC ->SNORD48 x Kt-46.hma +>SNORD48 revised 2 extra bases on 5 end x Kt-c-di-GMP-II.cac GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC ->SNORD48 x Kt-CD-box.AGU +>SNORD48 revised 2 extra bases on 5 end x Kt-G2nA-SAM-riboswitch T. tengcongensi GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC -((((((.((.((((((((((.....)))).).).)))).((((...))))...)).)))))).... ((...(((((..((..((((.....)))).))((((.((((((...))))..)).))))))))))) -1.84962844849 diff -r 312edff152eb -r 487f438da099 test-data/segments_truncated.2.out.txt --- a/test-data/segments_truncated.2.out.txt Thu Mar 31 04:20:55 2016 -0400 +++ b/test-data/segments_truncated.2.out.txt Fri May 06 05:45:36 2016 -0400 @@ -1,5 +1,7 @@ ->C/D-box snoRNA (shuffle iteration 1) -agaggCGUGAUcccaacgUGAuggc -....((((.......))))...... ....(...((((.....)))))... -9.3900680542 ->Artificial double C/D K-turn construct (shuffle iteration 1) -uguucugucacggcacauaccuccggUGUGAUggUGAauaguaUGAgaaguaucgugugucagaggcccuaaUGUGAUgccuuaa +>CD-box snoRNA x Kt-CD-box.CGU +GCUCUGACCGAAAGGCGUGAUGAGC +((((....((.....))....)))) (((((((((....))...))))))) 2.49938964844 +>Artificial double CD K-turn construct x Kt-CD-box.UGU +GGGAGUCUUGUGAUGAGAAGUACUGGAUCUGAAGUAGCCCUUUUUGGGCUACUUGUGAUGAAACACUCAUGGUCUGAAGACUCCC +((((((((((((........))).((((((((((((((((.....))))))))(((......))).))).))))).))))))))) ((((((((...(((((..(....((..(((((((((((((.....))))))))...)))))..))....)..))))))))))))) -1.26037597656 +((((((((((((........))).((((((((((((((((.....))))))))(((......))).))).))))).))))))))) ((((((((...(((((..(....((..(((((((((((((.....))))))))...)))))..))....)..))))))))))))) -1.26037597656 diff -r 312edff152eb -r 487f438da099 test-data/segments_truncated.out.txt --- a/test-data/segments_truncated.out.txt Thu Mar 31 04:20:55 2016 -0400 +++ b/test-data/segments_truncated.out.txt Fri May 06 05:45:36 2016 -0400 @@ -1,6 +1,7 @@ ->C/D-box snoRNA +>CD-box snoRNA x Kt-CD-box.CGU GCUCUGACCGAAAGGCGUGAUGAGC -((((....((.....))....)))) (((((((((....))...))))))) 2.50072479248 ->Artificial double C/D K-turn construct +((((....((.....))....)))) (((((((((....))...))))))) 2.49938964844 +>Artificial double CD K-turn construct x Kt-CD-box.UGU GGGAGUCUUGUGAUGAGAAGUACUGGAUCUGAAGUAGCCCUUUUUGGGCUACUUGUGAUGAAACACUCAUGGUCUGAAGACUCCC -((((((((((((........))).((((((((((((((((.....))))))))(((......))).))).))))).))))))))) ((((((((...(((((..(....((..(((((((((((((.....))))))))...)))))..))....)..))))))))))))) -1.25102996826 +((((((((((((........))).((((((((((((((((.....))))))))(((......))).))).))))).))))))))) ((((((((...(((((..(....((..(((((((((((((.....))))))))...)))))..))....)..))))))))))))) -1.26037597656 +((((((((((((........))).((((((((((((((((.....))))))))(((......))).))).))))).))))))))) ((((((((...(((((..(....((..(((((((((((((.....))))))))...)))))..))....)..))))))))))))) -1.26037597656 diff -r 312edff152eb -r 487f438da099 utils_add-read-counts.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/utils_add-read-counts.xml Fri May 06 05:45:36 2016 -0400 @@ -0,0 +1,77 @@ + + Annotate sequences by adding the read counts from a bam file, within a region contained in the fasta header of the dbn file + + + macros.xml + + + + @REQUIREMENTS_UTILS@ + + + + @VERSION_COMMAND_UTILS@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff -r 312edff152eb -r 487f438da099 utils_estimate-energy.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/utils_estimate-energy.xml Fri May 06 05:45:36 2016 -0400 @@ -0,0 +1,139 @@ + + Estimates whether a certain Segment(Loop) is present and for which delta-G this transistion takes place + + + macros.xml + + + + @REQUIREMENTS_SMF@ + @REQUIREMENTS_UTILS@ + + + + echo $(@VERSION_COMMAND_SMF@)", "$(@VERSION_COMMAND_UTILS@) + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff -r 312edff152eb -r 487f438da099 utils_extract-boxed-sequences.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/utils_extract-boxed-sequences.xml Fri May 06 05:45:36 2016 -0400 @@ -0,0 +1,110 @@ + + Extracts boxed sequences from bed_input_file which has to be created with 'find-box', part of this utility + + + macros.xml + + + + @REQUIREMENTS_UTILS@ + + + + @VERSION_COMMAND_UTILS@ + + + + + + + + + + + + + + + + + + + + + + + + + + + seq +gagagaTTTTgagagaTTTTgagagagagagagagaCCCCgaga +``` + +Namely: + +```TTTTgagagaTTTTgagagagagagagagaCCCC +``` + +and + +``` TTTTgagagagagagagagaCCCC +``` + +This is an utility of the segmentation-fold package + ]]> + + + diff -r 312edff152eb -r 487f438da099 utils_filter-annotated-entries.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/utils_filter-annotated-entries.xml Fri May 06 05:45:36 2016 -0400 @@ -0,0 +1,80 @@ + + Split entries into two files based on whether they overlap annotations in a bed file + + + macros.xml + + + + @REQUIREMENTS_UTILS@ + + + + @VERSION_COMMAND_UTILS@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff -r 312edff152eb -r 487f438da099 utils_find-boxes.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/utils_find-boxes.xml Fri May 06 05:45:36 2016 -0400 @@ -0,0 +1,85 @@ + + Finds all occurances of two given boxes (sequence motifs) within a FASTA file + + + macros.xml + + + + @REQUIREMENTS_UTILS@ + + + + @VERSION_COMMAND_UTILS@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +