Format

Send to

Choose Destination
Nucleic Acids Res. 2015 Jan;43(Database issue):D1064-70. doi: 10.1093/nar/gku1002. Epub 2014 Oct 27.

HAMAP in 2015: updates to the protein family classification and annotation system.

Author information

1
Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, CMU, 1 rue Michel-Servet, CH-1211 Geneva 4, Switzerland.
2
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.
3
Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, CMU, 1 rue Michel-Servet, CH-1211 Geneva 4, Switzerland alan.bridge@isb-sib.ch.

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.

PMID:
25348399
PMCID:
PMC4383873
DOI:
10.1093/nar/gku1002
[Indexed for MEDLINE]
Free PMC Article

Supplemental Content

Full text links

Icon for Silverchair Information Systems Icon for PubMed Central
Loading ...
Support Center