Phobius and its Distributed Annotation Service (DAS)
by
Erik Sonnhammer(SBC)
→
Europe/Stockholm
RB35
RB35
Description
Phobius has been benchmarked as the most accurate transmembrane topology predictor on single sequences, in particular when signal peptides are treated as unknowns. In the 2004 Phobius publication it was found to be 10-23% more accurate than TMHMM, previously considered the most accurate program. Despite this, the awareness that TMHMM is deprecated and superseded by Phobius is poor. With this talk I hope that at least scientists at SBC will be informed, and hopefully will pass it on to external colleagues.
The novelty of Phobius was that it can predict both signal peptides and transmembrane segments. This allows it to discriminate between these two often confused features, and the accuracy improvement stems from this ability.
To illustrate how important this discrimination is, we carried out the following study: TMHMM and SignalP were applied to five complete proteomes. 30-65% of all SignalP predicted signal peptides and 25-35% of all TMHMM predicted transmembrane topologies overlapped. This casts doubt over the predictions for 5-10% of each proteome. Phobius resolves these conflicts by making an optimal choice between transmembrane segments and signal peptides. It also allows constrained and homology-enriched predictions.
To make Phobius accessible beyond the web servers phobius.cgb.ki.se and phobius.binf.ku.dk we have also set up a DAS (Distributed Annotation System) server at SBC. This service can be queried with the DAS protocol using any Uniprot accession number, and a topology prediction will be returned. I will describe the DAS system briefly and demonstrate the DAS registry at www.dasregistry.org which currently holds 264 services (62 for protein sequence).