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author davidmurphy
date Sat, 31 Mar 2012 16:07:07 -0400
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2 CodonLogo (http://recode.ucc.ie/CodonLogo) is a tool for creating sequence
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3 logos from biological sequence alignments. It can be run on the command line,
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4 as a standalone webserver or as a CGI webapp.
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7 For help on the command line interface run
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8 ./codonlogo --help
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10 To build a simple logo run
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11 ./codonlogo < cap.fa > logo.eps
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14 To run as a standalone webserver at localhost:8080
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15 ./codonlogo --server
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18 An example file of probabilities is included, examplepriorfile.txt
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19 It can be used with the following command.
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21 ./codonlogo --prior examplepriorfile.txt < cap.fa > logo.eps
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24 examplepriorfile contains the frequencies for codons in human CDS regions.
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27 There is a known issue with GPL Ghostscript 9.04 which affects some users which may cause ghostscript to segfault.
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28 This is not believed to be a problem with CodonLogo.
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29 This is being investigated. if you encounter this problem it's recommended to downgrade to version 9.01 or earlier of ghostscript.
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31 For converting files to a suitable format the following sites can be used:
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33 http://genome.nci.nih.gov/tools/reformat.html
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34 http://www-bimas.cit.nih.gov/molbio/readseq/
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39 -- Distribution and Modification --
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40 This package is distributed under the new BSD Open Source License.
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41 Please see the LICENSE.txt file for details on copyright and licensing.
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42 The CodonLogo source code can be downloaded from
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43 http://recode.ucc.ie/CodonLogo
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45 CodonLogo requires Python 2.6 or 2.7, the corebio python toolkit for
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46 computational biology (http://code.google.com/p/corebio), and the python
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47 array package 'numpy' (http://www.scipy.org/Download)