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HAMAP in 2015: updates to the protein family classification and annotation system
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 f...
Autores principales: | , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2014
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4383873/ https://www.ncbi.nlm.nih.gov/pubmed/25348399 http://dx.doi.org/10.1093/nar/gku1002 |
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author | Pedruzzi, Ivo Rivoire, Catherine Auchincloss, Andrea H. Coudert, Elisabeth Keller, Guillaume de Castro, Edouard Baratin, Delphine Cuche, Béatrice A. Bougueleret, Lydie Poux, Sylvain Redaschi, Nicole Xenarios, Ioannis Bridge, Alan |
author_facet | Pedruzzi, Ivo Rivoire, Catherine Auchincloss, Andrea H. Coudert, Elisabeth Keller, Guillaume de Castro, Edouard Baratin, Delphine Cuche, Béatrice A. Bougueleret, Lydie Poux, Sylvain Redaschi, Nicole Xenarios, Ioannis Bridge, Alan |
author_sort | Pedruzzi, Ivo |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-4383873 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2014 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-43838732015-04-08 HAMAP in 2015: updates to the protein family classification and annotation system Pedruzzi, Ivo Rivoire, Catherine Auchincloss, Andrea H. Coudert, Elisabeth Keller, Guillaume de Castro, Edouard Baratin, Delphine Cuche, Béatrice A. Bougueleret, Lydie Poux, Sylvain Redaschi, Nicole Xenarios, Ioannis Bridge, Alan Nucleic Acids Res Database Issue 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. Oxford University Press 2014-10-27 2015-01-28 /pmc/articles/PMC4383873/ /pubmed/25348399 http://dx.doi.org/10.1093/nar/gku1002 Text en © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research. https://creativecommons.org/licenses/by-nc/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/ (https://creativecommons.org/licenses/by-nc/4.0/) ), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com |
spellingShingle | Database Issue Pedruzzi, Ivo Rivoire, Catherine Auchincloss, Andrea H. Coudert, Elisabeth Keller, Guillaume de Castro, Edouard Baratin, Delphine Cuche, Béatrice A. Bougueleret, Lydie Poux, Sylvain Redaschi, Nicole Xenarios, Ioannis Bridge, Alan HAMAP in 2015: updates to the protein family classification and annotation system |
title | HAMAP in 2015: updates to the protein family classification and annotation system |
title_full | HAMAP in 2015: updates to the protein family classification and annotation system |
title_fullStr | HAMAP in 2015: updates to the protein family classification and annotation system |
title_full_unstemmed | HAMAP in 2015: updates to the protein family classification and annotation system |
title_short | HAMAP in 2015: updates to the protein family classification and annotation system |
title_sort | hamap in 2015: updates to the protein family classification and annotation system |
topic | Database Issue |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4383873/ https://www.ncbi.nlm.nih.gov/pubmed/25348399 http://dx.doi.org/10.1093/nar/gku1002 |
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