title: HAMAP in 2015: updates to the protein family classification and annotation system.
abstract: HAMAP (High-quality Automated and Manual Annotation of Proteins--available at http://hamap.expasy.org/) is a system for the automatic classification and annotation of protein sequences. HAMAP provides annotation of the same quality and detail as UniProtKB/Swiss-Prot, using manually curated profiles for protein sequence family classification and expert curated rules for functional annotation of family members. HAMAP data and tools are made available through our website and as part of the UniRule pipeline of UniProt, providing annotation for millions of unreviewed sequences of UniProtKB/TrEMBL. Here we report on the growth of HAMAP and updates to the HAMAP system since our last report in the NAR Database Issue of 2013. We continue to augment HAMAP with new family profiles and annotation rules as new protein families are characterized and annotated in UniProtKB/Swiss-Prot; the latest version of HAMAP (as of 3 September 2014) contains 1983 family classification profiles and 1998 annotation rules (up from 1780 and 1720). We demonstrate how the complex logic of HAMAP rules allows for precise annotation of individual functional variants within large homologous protein families. We also describe improvements to our web-based tool HAMAP-Scan which simplify the classification and annotation of sequences, and the incorporation of an improved sequence-profile search algorithm.
authors.affiliation: Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, CMU, 1 rue Michel-Servet, CH-1211 Geneva 4, Switzerland.
authors.forename: Ivo
authors.initials: I
authors.lastname: Pedruzzi
authors.affiliation: Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, CMU, 1 rue Michel-Servet, CH-1211 Geneva 4, Switzerland.
authors.forename: Catherine
authors.initials: C
authors.lastname: Rivoire
authors.affiliation: Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, CMU, 1 rue Michel-Servet, CH-1211 Geneva 4, Switzerland.
authors.forename: Andrea H
authors.initials: AH
authors.lastname: Auchincloss
authors.affiliation: Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, CMU, 1 rue Michel-Servet, CH-1211 Geneva 4, Switzerland.
authors.forename: Elisabeth
authors.initials: E
authors.lastname: Coudert
authors.affiliation: Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, CMU, 1 rue Michel-Servet, CH-1211 Geneva 4, Switzerland.
authors.forename: Guillaume
authors.initials: G
authors.lastname: Keller
authors.affiliation: Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, CMU, 1 rue Michel-Servet, CH-1211 Geneva 4, Switzerland.
authors.forename: Edouard
authors.initials: E
authors.lastname: de Castro
authors.affiliation: Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, CMU, 1 rue Michel-Servet, CH-1211 Geneva 4, Switzerland.
authors.forename: Delphine
authors.initials: D
authors.lastname: Baratin
authors.affiliation: Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, CMU, 1 rue Michel-Servet, CH-1211 Geneva 4, Switzerland.
authors.forename: Béatrice A
authors.initials: BA
authors.lastname: Cuche
authors.affiliation: Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, CMU, 1 rue Michel-Servet, CH-1211 Geneva 4, Switzerland.
authors.forename: Lydie
authors.initials: L
authors.lastname: Bougueleret
authors.affiliation: Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, CMU, 1 rue Michel-Servet, CH-1211 Geneva 4, Switzerland.
authors.forename: Sylvain
authors.initials: S
authors.lastname: Poux
authors.affiliation: Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, CMU, 1 rue Michel-Servet, CH-1211 Geneva 4, Switzerland.
authors.forename: Nicole
authors.initials: N
authors.lastname: Redaschi
authors.affiliation: Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, CMU, 1 rue Michel-Servet, CH-1211 Geneva 4, Switzerland Vital-IT Group, SIB Swiss Institute of Bioinformatics, CH-1015, Lausanne, Switzerland Center for Integrative Genomics, University of Lausanne, CH-1015, Lausanne, Switzerland Department of Biochemistry, University of Geneva, CH-1211 Geneva 4, Switzerland.
authors.forename: Ioannis
authors.initials: I
authors.lastname: Xenarios
authors.affiliation: Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, CMU, 1 rue Michel-Servet, CH-1211 Geneva 4, Switzerland alan.bridge@isb-sib.ch.
authors.forename: Alan
authors.initials: A
authors.lastname: Bridge
mesh_terms: D030562:Databases, Protein; D006801:Humans; D020407:Internet; D058977:Molecular Sequence Annotation; D011506:Proteins / Q000145:classification; D017386:Sequence Homology, Amino Acid
chemical_list: D011506:Proteins