HAMAP in 2013, new developments in the protein family classification and annotation system
Open Access
- 26 November 2012
- journal article
- research article
- Published by Oxford University Press (OUP) in Nucleic Acids Research
- Vol. 41 (D1), D584-D589
- https://doi.org/10.1093/nar/gks1157
Abstract
HAMAP (High-quality Automated and Manual Annotation of Proteins—available at http://hamap.expasy.org/) is a system for the classification and annotation of protein sequences. It consists of a collection of manually curated family profiles for protein classification, and associated annotation rules that specify annotations that apply to family members. HAMAP was originally developed to support the manual curation of UniProtKB/Swiss-Prot records describing microbial proteins. Here we describe new developments in HAMAP, including the extension of HAMAP to eukaryotic proteins, the use of HAMAP in the automated annotation of UniProtKB/TrEMBL, providing high-quality annotation for millions of protein sequences, and the future integration of HAMAP into a unified system for UniProtKB annotation, UniRule. HAMAP is continuously updated by expert curators with new family profiles and annotation rules as new protein families are characterized. The collection of HAMAP family classification profiles and annotation rules can be browsed and viewed on the HAMAP website, which also provides an interface to scan user sequences against HAMAP profiles.Keywords
This publication has 31 references indexed in Scilit:
- Reorganizing the protein space at the Universal Protein Resource (UniProt)Nucleic Acids Research, 2011
- InterPro in 2011: new developments in the family and domain prediction databaseNucleic Acids Research, 2011
- Systematizing the generation of missing metabolic knowledgeBiotechnology & Bioengineering, 2010
- A phylogeny-driven genomic encyclopaedia of Bacteria and ArchaeaNature, 2009
- PROSITE, a protein domain database for functional characterization and annotationNucleic Acids Research, 2009
- HAMAP: a database of completely sequenced microbial proteome sets and manually curated microbial protein families in UniProtKB/Swiss-ProtNucleic Acids Research, 2008
- Toward an Online Repository of Standard Operating Procedures (SOPs) for (Meta)genomic AnnotationOMICS: A Journal of Integrative Biology, 2008
- TIGRFAMs and Genome Properties: tools for the assignment of molecular function and biological process in prokaryotic genomesNucleic Acids Research, 2006
- Towards multidimensional genome annotationNature Reviews Genetics, 2006
- Basic Local Alignment Search ToolJournal of Molecular Biology, 1990