INGA: protein function prediction combining interaction networks, domain assignments and sequence similarity.

Identifying protein functions can be useful for numerous applications in biology. The prediction of gene ontology (GO) functional terms from sequence remains however a challenging task, as shown by the recent CAFA experiments. Here we present INGA, a web server developed to predict protein function from a combination of three orthogonal approaches. Sequence similarity and domain architecture searches are combined with protein-protein interaction network data to derive consensus predictions for GO terms using functional enrichment. The INGA server can be queried both programmatically through RESTful services and through a web interface designed for usability. The latter provides output supporting the GO term predictions with the annotating sequences. INGA is validated on the CAFA-1 data set and was recently shown to perform consistently well in the CAFA-2 blind test. The INGA web server is available from URL: http://protein.bio.unipd.it/inga.