title: INGA: protein function prediction combining interaction networks, domain assignments and sequence similarity.
abstract: 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.
authors.affiliation: Department of Biomedical Sciences, University of Padua, Padua 35121, Italy.
authors.forename: Damiano
authors.initials: D
authors.lastname: Piovesan
authors.affiliation: Department of Biomedical Sciences, University of Padua, Padua 35121, Italy Department of Information Engineering, University of Padua, Padua 35121, Italy.
authors.forename: Manuel
authors.initials: M
authors.lastname: Giollo
authors.affiliation: Department of Women's and Children's Health, University of Padua, Padua 35128, Italy.
authors.forename: Emanuela
authors.initials: E
authors.lastname: Leonardi
authors.affiliation: Department of Information Engineering, University of Padua, Padua 35121, Italy.
authors.forename: Carlo
authors.initials: C
authors.lastname: Ferrari
authors.affiliation: Department of Biomedical Sciences, University of Padua, Padua 35121, Italy CNR Institute of Neuroscience, Padua 35121, Italy silvio.tosatto@unipd.it.
authors.forename: Silvio C E
authors.identifier: http://orcid.org/0000-0003-4525-7793
authors.initials: SC
authors.lastname: Tosatto
mesh_terms: D063990:Gene Ontology; D006801:Humans; D020407:Internet; D058977:Molecular Sequence Annotation; D025941:Protein Interaction Mapping; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000235:genetics / Q000502:physiology; D017386:Sequence Homology, Amino Acid; D012984:Software
chemical_list: D011506:Proteins