A bioruby plugin for running the transmembrane domain predictor TMHMM automatically on multiple sequences in a FASTA file and manipulation of the results.
gem install bio-tm_hmm
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
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:
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
This Biogem is published at http://biogems.info/index.html#bio-tm_hmm
Copyright (c) 2012 Ben J Woodcroft. See LICENSE.txt for further details.