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A bioruby plugin for running and parsing octopus, available from 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:

  • a working install of SPOCTOPUS

  • NCBI legacy blast

Binaries for these must be accessible in the PATH.

Contributing to bio-octopus

  • Check out the latest master to make sure the feature hasn’t been implemented or the bug hasn’t been fixed yet

  • Check out the issue tracker to make sure someone already hasn’t requested it and/or contributed it

  • Fork the project

  • Start a feature/bugfix branch

  • Commit and push until you are happy with your contribution

  • Make sure to add tests for it. This is important so I don’t break it in a future version unintentionally.

  • Please try not to mess with the Rakefile, version, or history. If you want to have your own version, or is otherwise necessary, that is fine, but please isolate to its own commit so I can cherry-pick around it.

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


Running and parsing of the protein transmembrane domain predictor octopus







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