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author davidmurphy
date Fri, 20 Jan 2012 09:03:40 -0500
parents 4d47ab2b7bcc
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2 CodonLogo (http://recode.ucc.ie/CodonLogo) is a tool for creating sequence 2 CodonLogo (http://recode.ucc.ie/CodonLogo) is a tool for creating sequence
3 logos from biological sequence alignments. It can be run on the command line, 3 logos from biological sequence alignments. It can be run from the command line as a standalone webserver or as a CGI webapp.
4 as a standalone webserver or as a CGI webapp.
5 4
6 5
7 For help on the command line interface run 6 For help on the command line interface run
8 ./codonlogo --help 7 ./codonlogo --help
9 8
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18 An example file of probabilities is included, examplepriorfile.txt 17 An example file of probabilities is included, examplepriorfile.txt
19 It can be used with the following command. 18 It can be used with the following command.
20 19
21 ./codonlogo --prior examplepriorfile.txt < cap.fa > logo.eps 20 ./codonlogo --prior ./examples/Escherichiacoli.txt < cap.fa > logo.eps
22 21
23 22
24 There is a known issue with GPL Ghostscript 9.04 which affects some users which may cause ghostscript to segfault. 23 examplepriorfile contains the frequencies for codons in human CDS regions.
25 This is not believed to be a problem with CodonLogo. 24
26 This is being investigated. if you encounter this problem it's recommended to downgrade to version 9.01 or earlier of ghostscript. 25
26 KNOWN ISSUES:
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28 There is a known issue with GPL Ghostscript 9.04 which affects some users which may cause ghostscript to segfault or prevent codonlogos from being generated in anything other than eps format.
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30 This is believed to be an issue with ghostscript and a bug report has been submitted to the ghostscript mailing list.
31 This is being investigated. if you encounter this problem it's recommended to downgrade to version 9.01 of ghostscript or earlier .
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35 For converting files to a suitable format the following sites can be used:
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37 http://genome.nci.nih.gov/tools/reformat.html
38 http://www-bimas.cit.nih.gov/molbio/readseq/
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27 40
28 41
29 42
30 -- Distribution and Modification -- 43 -- Distribution and Modification --
31 This package is distributed under the new BSD Open Source License. 44 This package is distributed under the new BSD Open Source License.