ArticleNucleic acids research2015
HAMAP in 2015: updates to the protein family classification and annotation system.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 109 papers.
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109 citing papers in PubMed.
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- Comparative genomics analyses reveal genomic variation and evolutionary adaptation in Dendrobium orchids.Nature communications · 2025Article
- A genomic atlas of the human gut virome elucidates genetic factors shaping host interactions.bioRxiv : the preprint server for biology · 2025Article
- Subtractive Proteomic Approaches to Identify Drug Targets: An Analysis on Hypothetical Proteins of Multidrug-ResistantACS omega · 2025Article
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- Unraveling the microbial diversity of bovine liver abscesses: isolation, identification, and genomic characterization of theMicrobiology spectrum · 2025Article
- Complex system modeling reveals oxalate homeostasis is driven by diverse oxalate-degrading bacteria.eLife · 2025Article
- Computational studies reveal structural characterization and novel families of Puccinia striiformis f. sp. tritici effectors.PLoS computational biology · 2025Article
- Comprehensive genome annotation of Bombyx mori p50ma strain, a newly developed standard strain.Scientific data · 2025Article
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- InterPro: the protein sequence classification resource in 2025.Nucleic acids research · 2025Article
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- Surveillance of coronaviruses in wild aquatic birds in Hong Kong: expanded genetic diversity and discovery of novel subgenus in theVirus evolution · 2025Article
- Deep learning methods for protein function prediction.Proteomics · 2025Review
49 more citing papers are in PubMed but not listed here.
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13 authors.
Funding
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.
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