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SUPERFAMILY—sophisticated comparative genomics, data mining, visualization and phylogeny
SUPERFAMILY provides structural, functional and evolutionary information for proteins from all completely sequenced genomes, and large sequence collections such as UniProt. Protein domain assignments for over 900 genomes are included in the database, which can be accessed at http://supfam.org/. Hidd...
Autores principales: | , , , , , , , |
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Formato: | Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2009
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2686452/ https://www.ncbi.nlm.nih.gov/pubmed/19036790 http://dx.doi.org/10.1093/nar/gkn762 |
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author | Wilson, Derek Pethica, Ralph Zhou, Yiduo Talbot, Charles Vogel, Christine Madera, Martin Chothia, Cyrus Gough, Julian |
author_facet | Wilson, Derek Pethica, Ralph Zhou, Yiduo Talbot, Charles Vogel, Christine Madera, Martin Chothia, Cyrus Gough, Julian |
author_sort | Wilson, Derek |
collection | PubMed |
description | SUPERFAMILY provides structural, functional and evolutionary information for proteins from all completely sequenced genomes, and large sequence collections such as UniProt. Protein domain assignments for over 900 genomes are included in the database, which can be accessed at http://supfam.org/. Hidden Markov models based on Structural Classification of Proteins (SCOP) domain definitions at the superfamily level are used to provide structural annotation. We recently produced a new model library based on SCOP 1.73. Family level assignments are also available. From the web site users can submit sequences for SCOP domain classification; search for keywords such as superfamilies, families, organism names, models and sequence identifiers; find over- and underrepresented families or superfamilies within a genome relative to other genomes or groups of genomes; compare domain architectures across selections of genomes and finally build multiple sequence alignments between Protein Data Bank (PDB), genomic and custom sequences. Recent extensions to the database include InterPro abstracts and Gene Ontology terms for superfamiles, taxonomic visualization of the distribution of families across the tree of life, searches for functionally similar domain architectures and phylogenetic trees. The database, models and associated scripts are available for download from the ftp site. |
format | Text |
id | pubmed-2686452 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2009 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-26864522009-05-26 SUPERFAMILY—sophisticated comparative genomics, data mining, visualization and phylogeny Wilson, Derek Pethica, Ralph Zhou, Yiduo Talbot, Charles Vogel, Christine Madera, Martin Chothia, Cyrus Gough, Julian Nucleic Acids Res Articles SUPERFAMILY provides structural, functional and evolutionary information for proteins from all completely sequenced genomes, and large sequence collections such as UniProt. Protein domain assignments for over 900 genomes are included in the database, which can be accessed at http://supfam.org/. Hidden Markov models based on Structural Classification of Proteins (SCOP) domain definitions at the superfamily level are used to provide structural annotation. We recently produced a new model library based on SCOP 1.73. Family level assignments are also available. From the web site users can submit sequences for SCOP domain classification; search for keywords such as superfamilies, families, organism names, models and sequence identifiers; find over- and underrepresented families or superfamilies within a genome relative to other genomes or groups of genomes; compare domain architectures across selections of genomes and finally build multiple sequence alignments between Protein Data Bank (PDB), genomic and custom sequences. Recent extensions to the database include InterPro abstracts and Gene Ontology terms for superfamiles, taxonomic visualization of the distribution of families across the tree of life, searches for functionally similar domain architectures and phylogenetic trees. The database, models and associated scripts are available for download from the ftp site. Oxford University Press 2009-01 2008-11-26 /pmc/articles/PMC2686452/ /pubmed/19036790 http://dx.doi.org/10.1093/nar/gkn762 Text en © 2008 The Author(s) http://creativecommons.org/licenses/by-nc/2.0/uk/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Articles Wilson, Derek Pethica, Ralph Zhou, Yiduo Talbot, Charles Vogel, Christine Madera, Martin Chothia, Cyrus Gough, Julian SUPERFAMILY—sophisticated comparative genomics, data mining, visualization and phylogeny |
title | SUPERFAMILY—sophisticated comparative genomics, data mining, visualization and phylogeny |
title_full | SUPERFAMILY—sophisticated comparative genomics, data mining, visualization and phylogeny |
title_fullStr | SUPERFAMILY—sophisticated comparative genomics, data mining, visualization and phylogeny |
title_full_unstemmed | SUPERFAMILY—sophisticated comparative genomics, data mining, visualization and phylogeny |
title_short | SUPERFAMILY—sophisticated comparative genomics, data mining, visualization and phylogeny |
title_sort | superfamily—sophisticated comparative genomics, data mining, visualization and phylogeny |
topic | Articles |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2686452/ https://www.ncbi.nlm.nih.gov/pubmed/19036790 http://dx.doi.org/10.1093/nar/gkn762 |
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