bio-octopus

A bioruby plugin for running and parsing octopus, available from octopus.cbr.su.se/ Currently, the plugin is not Ruby 1.9 (only 1.8) compatible, because of the dependency on the rio gem.

To run it as a script, a fasta file of sequences to predict, and a database formatted in legacy blast database format needs to be specified:

$ /usr/local/rvm/gems/ruby-1.8.7-p334/gems/bio-octopus-0.1.0/bin/biooctopus my.fasta /blastdb/UniProt2011_04/uniprot_sprot.fasta

Output are topology predictions, including signal peptide and transmembrane domain predictions. If that is not the best format for you, look at the script file and modify it - it is just a front-end. Also required are:

Binaries for these must be accessible in the PATH.

Contributing to bio-octopus

Copyright © 2011 Ben J Woodcroft. See LICENSE.txt for further details.