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8
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1
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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 from the command line as a standalone webserver or as a CGI webapp.
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4
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5
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6 For help on the command line interface run
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7 ./codonlogo --help
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8
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9 To build a simple logo run
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10 ./codonlogo < cap.fa > logo.eps
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11
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12
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13 To run as a standalone webserver at localhost:8080
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14 ./codonlogo --server
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15
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16
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17 An example file of probabilities is included, examplepriorfile.txt
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18 It can be used with the following command.
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19
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20 ./codonlogo --prior ./examples/Escherichiacoli.txt < cap.fa > logo.eps
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21
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22
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23 examplepriorfile contains the frequencies for codons in human CDS regions.
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24
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25
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26 KNOWN ISSUES:
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27
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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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29
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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.
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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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32
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33
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34
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35 For converting files to a suitable format the following sites can be used:
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36
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37 http://genome.nci.nih.gov/tools/reformat.html
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38 http://www-bimas.cit.nih.gov/molbio/readseq/
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39
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40
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41
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42
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43 -- Distribution and Modification --
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44 This package is distributed under the new BSD Open Source License.
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45 Please see the LICENSE.txt file for details on copyright and licensing.
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46 The CodonLogo source code can be downloaded from
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47 http://recode.ucc.ie/CodonLogo
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48
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49 CodonLogo requires Python 2.6 or 2.7, the corebio python toolkit for
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50 computational biology (http://code.google.com/p/corebio), and the python
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51 array package 'numpy' (http://www.scipy.org/Download)
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