Phobius

Downloads

Phobius is freely available for local installation for academic use. The bundle contains the phobius.pl command-line predictor, the decoder and the model, and runs on any Unix with Perl.

phobius101_linux.tgz — 0.6 MB

Phobius is intended for academic users only. Other users are requested to contact Erik Sonnhammer at Erik.Sonnhammer@gmail.com. By downloading you agree to use the software only for private study, education or nonprofit research.

phobius101_linux.tgz (0.6 MB)

HomologHMM

HomologHMM, the feature prediction method behind PolyPhobius, is distributed under the GPL, packaged with a slightly modified copy of BioJava, redistributed under the LGPL.

For a standalone copy of PolyPhobius you also need the model file from the Phobius package.

Training data

Phobius was trained on four types of protein, each divided into ten cross-validation sets:

Transmembrane proteins with signal peptides: m[0-9].faa
Transmembrane proteins without signal peptides: t[0-9].faa
Non-transmembrane proteins with signal peptides: s[0-9].faa
Non-transmembrane proteins without signal peptides: g[0-9].faa

The sets are in labelled FASTA format.

This web service

The source for this server is at github.com/statisticalbiotechnology/phobius_www. The prediction model itself is licensed separately and is not included.