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

By I. Pedruzzi, C. Rivoire, A. Auchincloss, E. Coudert, G. Keller, Edouard De Castro, Delphine Baratin, Béatrice A. Cuche, L. Bougueleret, S. Poux and 3 more. 2014

152 citations recorded by the source corpus.

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.

Subfields: Molecular Biology

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Citations in the corpus

UniProt: the universal protein knowledgebase (2016, methodology): “InterPro integrates signatures from the HAMAP (19) and PIRSF (20) projects within the UniProt Consortium.”
UniProt: a hub for protein information (2014, methodology): “As an example the HAMAP signature MF 01864 see Figure 4, which encapsulates the information from only seven peer-reviewed publications covering four experimentally characterized proteins that serve as templates to annotate the function of the bacterial tRNA-2-methylthioN(6)-dimethylallyladenosine sy”
InterPro in 2017—beyond protein family and domain annotations (2016, background): “The signatures are provided by 14 different member databases: 12 of these are long-standing members of the InterPro Consortium (CATH-Gene3D (3), HAMAP (4), PANTHER (5), Pfam (6), PIRSF (7), PRINTS (8), ProDom (9), PROSITE Patterns (10), PROSITE Profiles (10), SMART (11), SUPERFAMILY (12) and TIGRFAM”
The InterPro protein families and domains database: 20 years on (2020, background): “InterPro integrates 13 protein signature databases into one central resource: CATH-Gene3D (1), the Conserved Domains Database (CDD) (2), HAMAP (3), PANTHER (4), Pfam (5), PIRSF (6), PRINTS (7), PROSITE Patterns (8), PROSITE Profiles (8), SMART (9), the Structure–Function Linkage Database (SFLD) (10)”
RegulonDB version 9.0: high-level integration of gene regulation, coexpression, motif clustering and beyond (2015, background): “In addition, TFs specifically associated with E. coli K-12 and deposited in the DBD, HAMAP (10), Superfamily DB (11) and PFAM (12) databases were retrieved.”
InterPro in 2022 (2022, unknown): “InterPro combines 13 protein signature databases into one central resource: CATH-Gene3D (1), the Conserved Domains Database (CDD) (2), HAMAP (3), PANTHER (4), Pfam (5), PIRSF (6), PRINTS (7), PROSITE Patterns (8), PROSITE Profiles (8), SMART (9), the Structure– Function Linkage Database (SFLD) (10),”
The SIB Swiss Institute of Bioinformatics’ resources: focus on curated databases (2015, background): “org) (26), which are both available as web-based resources for external users to annotate their own protein and proteome sequences.”
InterPro in 2019: improving coverage, classification and access to protein sequence annotations (2018, methodology): “Launched in 1999, InterPro is derived from 14 different specialist member databases: CATH-Gene3D (2), the Conserved Do-mains Database (CDD) (3), HAMAP (4), PANTHER (5), Pfam (6), PIRSF (7), PRINTS (8), ProDom (9), PROSITE Patterns (10), PROSITE Profiles (10), SMART (11), the Structure–Function Linka”