bio-tm_hmm

Build Status

A bioruby plugin for running the transmembrane domain predictor TMHMM automatically on multiple sequences in a FASTA file and manipulation of the results.

Installation

gem install bio-tm_hmm

Usage

Usage: bio-tm_hmm [-f NUM] [-g NUM] [fasta_filename]

    fasta file can also be piped in on STDIN.
    without arguments, a description of the transmembrane domains is printed out for each input sequence
    -f MIN_TRANSMEMBRANE_DOMAINS,    Print those sequences that have at _least_ MIN_TRANSMEMBRANE_DOMAINS transmembrane domain(s). Prints out the sequences in FASTA format.
        --filter-in
    -g MAX_TRANSMEMBRANE_DOMAINS,    Print those sequences that have at _most_ MAX_TRANSMEMBRANE_DOMAINS transmembrane domain(s). Prints out the sequences in FASTA format.
        --filter-out

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 don't (converse is -g). For instance, to filter out all sequences that have less than 2 predicted transmembrane domains:

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:

Organellar proteomics reveals hundreds of novel nuclear proteins in the malaria parasite Plasmodium falciparum

Sophie C Oehring, Ben J Woodcroft, Suzette Moes, Johanna Wetzel, Olivier Dietz, Andreas Pulfer, Chaitali Dekiwadia, Pascal Maeser, Christian Flueck, Kathrin Witmer, Nicolas MB Brancucci, Igor Niederwieser, Paul Jenoe, Stuart A Ralph and Till S Voss

Genome Biology 2012, 13:R108 doi:10.1186/gb-2012-13-11-r108

Biogems.info

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

Copyright

Copyright (c) 2012 Ben J Woodcroft. See LICENSE.txt for further details.