Mercurial > repos > bgruening > glimmer

diff glimmer_build-icm.xml @ 6:a07c49839f31

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author bgruening
date Sun, 09 Jun 2013 07:57:22 -0400
parents 8ddf54417ade
children ec5cf10b8db7
line wrap: on
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--- a/glimmer_build-icm.xml	Fri Jun 07 10:02:12 2013 -0400
+++ b/glimmer_build-icm.xml	Sun Jun 09 07:57:22 2013 -0400
@@ -1,5 +1,5 @@
-<tool id="glimmer_build-icm" name="ICM builder" version="0.1">
-    <description>(glimmer)</description>
+<tool id="glimmer_build-icm" name="Glimmer ICM builder" version="0.2">
+    <description></description>
     <requirements>
         <requirement type="package" version="3.02b">glimmer</requirement>
     </requirements>
@@ -74,40 +74,41 @@
 
 **What it does**
 
-	This program constructs an interpolated context model (ICM) from an input set of sequences.
-	This model can be used by Glimmer3 to predict genes.
+This program constructs an interpolated context model (ICM) from an input set of sequences.
+
+This model can be used by Glimmer3 to predict genes.
+
+**TIP** To extract CDS from a GenBank file use the tool *Extract ORF from a GenBank file*.
 
 -----
 
-
 **Example**
 
-* input::
+*Input*::
 
-	-Genome Sequence
+	- Genome Sequence
 
-	>CELF22B7  C.aenorhabditis elegans (Bristol N2) cosmid F22B7
-	GATCCTTGTAGATTTTGAATTTGAAGTTTTTTCTCATTCCAAAACTCTGT
-	GATCTGAAATAAAATGTCTCAAAAAAATAGAAGAAAACATTGCTTTATAT
-	TTATCAGTTATGGTTTTCAAAATTTTCTGACATACCGTTTTGCTTCTTTT
-	TTTCTCATCTTCTTCAAATATCAATTGTGATAATCTGACTCCTAACAATC
-	GAATTTCTTTTCCTTTTTCTTTTTCCAACAACTCCAGTGAGAACTTTTGA
-	ATATCTTCAAGTGACTTCACCACATCAGAAGGTGTCAACGATCTTGTGAG
-	AACATCGAATGAAGATAATTTTAATTTTAGAGTTACAGTTTTTCCTCCGA
-	CAATTCCTGATTTACGAACATCTTCTTCAAGCATTCTACAGATTTCTTGA
-	TGCTCTTCTAGGAGGATGTTGAAATCCGAAGTTGGAGAAAAAGTTCTCTC
-	AACTGAAATGCTTTTTCTTCGTGGATCCGATTCAGATGGACGACCTGGCA
-	GTCCGAGAGCCGTTCGAAGGAAAGATTCTTGTGAGAGAGGCGTGAAACAC
-	AAAGGGTATAGGTTCTTCTTCAGATTCATATCACCAACAGTTTGAATATC
-	CATTGCTTTCAGTTGAGCTTCGCATACACGACCAATTCCTCCAACCTAAA
-	AAATTATCTAGGTAAAACTAGAAGGTTATGCTTTAATAGTCTCACCTTAC
-	GAATCGGTAAATCCTTCAAAAACTCCATAATCGCGTTTTTATCATTTTCT
-	.....
+		>CELF22B7  C.aenorhabditis elegans (Bristol N2) cosmid F22B7
+		GATCCTTGTAGATTTTGAATTTGAAGTTTTTTCTCATTCCAAAACTCTGT
+		GATCTGAAATAAAATGTCTCAAAAAAATAGAAGAAAACATTGCTTTATAT
+		TTATCAGTTATGGTTTTCAAAATTTTCTGACATACCGTTTTGCTTCTTTT
+		TTTCTCATCTTCTTCAAATATCAATTGTGATAATCTGACTCCTAACAATC
+		GAATTTCTTTTCCTTTTTCTTTTTCCAACAACTCCAGTGAGAACTTTTGA
+		ATATCTTCAAGTGACTTCACCACATCAGAAGGTGTCAACGATCTTGTGAG
+		AACATCGAATGAAGATAATTTTAATTTTAGAGTTACAGTTTTTCCTCCGA
+		CAATTCCTGATTTACGAACATCTTCTTCAAGCATTCTACAGATTTCTTGA
+		TGCTCTTCTAGGAGGATGTTGAAATCCGAAGTTGGAGAAAAAGTTCTCTC
+		AACTGAAATGCTTTTTCTTCGTGGATCCGATTCAGATGGACGACCTGGCA
+		GTCCGAGAGCCGTTCGAAGGAAAGATTCTTGTGAGAGAGGCGTGAAACAC
+		AAAGGGTATAGGTTCTTCTTCAGATTCATATCACCAACAGTTTGAATATC
+		CATTGCTTTCAGTTGAGCTTCGCATACACGACCAATTCCTCCAACCTAAA
+		AAATTATCTAGGTAAAACTAGAAGGTTATGCTTTAATAGTCTCACCTTAC
+		GAATCGGTAAATCCTTCAAAAACTCCATAATCGCGTTTTTATCATTTTCT
+		.....
 
-* output:
+*Output*::
 	interpolated context model (ICM)
 
-
 -------
 
 **References**