A bioruby plugin for running TMHMM automatically on multiple sequences in a FASTA file and manipulation of the results
Note: this software is under active development!
gem install bio-tm_hmm
Where my.fasta is a FASTA file with one or more protein sequences in it. Output will be a description of the transmembrane domains predicted by TMHMM.
Other options include -f for printing out the fasta sequences that have some number of transmembrane domains in them, and ignoring those that done (converse is -g)
bio-tm_hmm -f 2 <my.fasta
To use the library
The API doc is online. For more code examples see also the test files in the source tree.
Project home page
Information on the source tree, documentation, issues and how to contribute, see
The BioRuby community is on IRC server: irc.freenode.org, channel: #bioruby.
If you use this software, please cite one of
[BioRuby: bioinformatics software for the Ruby programming language](dx.doi.org/10.1093/bioinformatics/btq475)
[Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics](dx.doi.org/10.1093/bioinformatics/bts080)
This Biogem is published at biogems.info/index.html#bio-tm_hmm
Copyright © 2012 Ben J Woodcroft. See LICENSE.txt for further details.