title: SIFTER search: a web server for accurate phylogeny-based protein function prediction.
abstract: We are awash in proteins discovered through high-throughput sequencing projects. As only a minuscule fraction of these have been experimentally characterized, computational methods are widely used for automated annotation. Here, we introduce a user-friendly web interface for accurate protein function prediction using the SIFTER algorithm. SIFTER is a state-of-the-art sequence-based gene molecular function prediction algorithm that uses a statistical model of function evolution to incorporate annotations throughout the phylogenetic tree. Due to the resources needed by the SIFTER algorithm, running SIFTER locally is not trivial for most users, especially for large-scale problems. The SIFTER web server thus provides access to precomputed predictions on 16 863 537 proteins from 232 403 species. Users can explore SIFTER predictions with queries for proteins, species, functions, and homologs of sequences not in the precomputed prediction set. The SIFTER web server is accessible at http://sifter.berkeley.edu/ and the source code can be downloaded.
authors.affiliation: Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA.
authors.forename: Sayed M
authors.initials: SM
authors.lastname: Sahraeian
authors.affiliation: Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA.
authors.forename: Kevin R
authors.initials: KR
authors.lastname: Luo
authors.affiliation: Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA brenner@compbio.berkeley.edu.
authors.forename: Steven E
authors.initials: SE
authors.lastname: Brenner
mesh_terms: D000465:Algorithms; D020407:Internet; D015233:Models, Statistical; D058977:Molecular Sequence Annotation; D010802:Phylogeny; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000145:classification* / Q000502:physiology*; D017386:Sequence Homology, Amino Acid; D012984:Software
chemical_list: D011506:Proteins