bio-tm_hmm

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!

Installation

gem install bio-tm_hmm

Usage

bio-tm_hmm my.fasta

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

Developers

To use the library

require 'bio-tm_hmm'

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

http://github.com/wwood/bioruby-tm_hmm

The BioRuby community is on IRC server: irc.freenode.org, channel: #bioruby.

Cite

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)

Biogems.info

This Biogem is published at biogems.info/index.html#bio-tm_hmm