Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2013 Jan;41(Database issue):D584-9.
doi: 10.1093/nar/gks1157. Epub 2012 Nov 27.

HAMAP in 2013, new developments in the protein family classification and annotation system

Ivo Pedruzzi  1 , Catherine Rivoire, Andrea H Auchincloss, Elisabeth Coudert, Guillaume Keller, Edouard de Castro, Delphine Baratin, Béatrice A Cuche, Lydie Bougueleret, Sylvain Poux, Nicole Redaschi, Ioannis Xenarios, Alan Bridge; UniProt Consortium
Affiliations

HAMAP in 2013, new developments in the protein family classification and annotation system

Ivo Pedruzzi et al. Nucleic Acids Res. 2013 Jan.

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.

PubMed Disclaimer

Figures

Figure 1.
Figure 1.
A sample HAMAP profile page. The page provides information such as a family name and description, taxonomic range of the hits, associated annotation rule(s), cross-references to InterPro and access to matching proteins in UniProtKB. Additionally, links on the page provide access to (a) the actual family classification profile, (b) the seed alignment that was used to generate the profile with highlighted features from the annotation rule, (c) an interactive, graphical view of the score distribution of matching proteins, including those that fall below the trusted cutoff, and (d) an expandable view of the taxonomic distribution of matching proteins in UniProtKB.
See this image and copyright information in PMC

References

    1. Wu D, Hugenholtz P, Mavromatis K, Pukall R, Dalin E, Ivanova NN, Kunin V, Goodwin L, Wu M, Tindall BJ, et al. A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature. 2009;462:1056–1060. - PMC - PubMed
    1. Reed JL, Famili I, Thiele I, Palsson BO. Towards multidimensional genome annotation. Nat. Rev. Genet. 2006;7:130–141. - PubMed
    1. Orth JD, Palsson BO. Systematizing the generation of missing metabolic knowledge. Biotechnol. Bioeng. 2010;107:403–412. - PMC - PubMed
    1. Karsch-Mizrachi I, Nakamura Y, Cochrane G. The International Nucleotide Sequence Database Collaboration. Nucleic Acids Res. 2012;40:D33–D37. - PMC - PubMed
    1. Angiuoli SV, Gussman A, Klimke W, Cochrane G, Field D, Garrity G, Kodira CD, Kyrpides N, Madupu R, Markowitz V, et al. Toward an online repository of Standard Operating Procedures (SOPs) for (meta)genomic annotation. OMICS. 2008;12:137–141. - PMC - PubMed

Publication types