Mercurial > repos > davidmurphy > codonlogo
comparison README.txt~ @ 8:5149eb3a89c2
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author | davidmurphy |
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date | Fri, 20 Jan 2012 09:03:40 -0500 |
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1 | |
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, | |
4 as a standalone webserver or as a CGI webapp. | |
5 | |
6 | |
7 For help on the command line interface run | |
8 ./codonlogo --help | |
9 | |
10 To build a simple logo run | |
11 ./codonlogo < cap.fa > logo.eps | |
12 | |
13 | |
14 To run as a standalone webserver at localhost:8080 | |
15 ./codonlogo --server | |
16 | |
17 | |
18 An example file of probabilities is included, examplepriorfile.txt | |
19 It can be used with the following command. | |
20 | |
21 ./codonlogo --prior examplepriorfile.txt < cap.fa > logo.eps | |
22 | |
23 | |
24 examplepriorfile contains the frequencies for codons in human CDS regions. | |
25 | |
26 | |
27 There is a known issue with GPL Ghostscript 9.04 which affects some users which may cause ghostscript to segfault. | |
28 This is not believed to be a problem with CodonLogo. | |
29 This is being investigated. if you encounter this problem it's recommended to downgrade to version 9.01 or earlier of ghostscript. | |
30 | |
31 For converting files to a suitable format the following sites can be used: | |
32 | |
33 http://genome.nci.nih.gov/tools/reformat.html | |
34 http://www-bimas.cit.nih.gov/molbio/readseq/ | |
35 | |
36 | |
37 | |
38 | |
39 -- Distribution and Modification -- | |
40 This package is distributed under the new BSD Open Source License. | |
41 Please see the LICENSE.txt file for details on copyright and licensing. | |
42 The CodonLogo source code can be downloaded from | |
43 http://recode.ucc.ie/CodonLogo | |
44 | |
45 CodonLogo requires Python 2.6 or 2.7, the corebio python toolkit for | |
46 computational biology (http://code.google.com/p/corebio), and the python | |
47 array package 'numpy' (http://www.scipy.org/Download) |