bio-tm_hmm¶ ↑
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
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:
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 biogems.info/index.html#bio-tm_hmm
Copyright¶ ↑
Copyright © 2012 Ben J Woodcroft. See LICENSE.txt for further details.