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SUPERFAMILY 1.75 including a domain-centric gene ontology method
The SUPERFAMILY resource provides protein domain assignments at the structural classification of protein (SCOP) superfamily level for over 1400 completely sequenced genomes, over 120 metagenomes and other gene collections such as UniProt. All models and assignments are available to browse and downlo...
Autores principales: | , , , , , , |
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Formato: | Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2011
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013712/ https://www.ncbi.nlm.nih.gov/pubmed/21062816 http://dx.doi.org/10.1093/nar/gkq1130 |
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author | de Lima Morais, David A. Fang, Hai Rackham, Owen J. L. Wilson, Derek Pethica, Ralph Chothia, Cyrus Gough, Julian |
author_facet | de Lima Morais, David A. Fang, Hai Rackham, Owen J. L. Wilson, Derek Pethica, Ralph Chothia, Cyrus Gough, Julian |
author_sort | de Lima Morais, David A. |
collection | PubMed |
description | The SUPERFAMILY resource provides protein domain assignments at the structural classification of protein (SCOP) superfamily level for over 1400 completely sequenced genomes, over 120 metagenomes and other gene collections such as UniProt. All models and assignments are available to browse and download at http://supfam.org. A new hidden Markov model library based on SCOP 1.75 has been created and a previously ignored class of SCOP, coiled coils, is now included. Our scoring component now uses HMMER3, which is in orders of magnitude faster and produces superior results. A cloud-based pipeline was implemented and is publicly available at Amazon web services elastic computer cloud. The SUPERFAMILY reference tree of life has been improved allowing the user to highlight a chosen superfamily, family or domain architecture on the tree of life. The most significant advance in SUPERFAMILY is that now it contains a domain-based gene ontology (GO) at the superfamily and family levels. A new methodology was developed to ensure a high quality GO annotation. The new methodology is general purpose and has been used to produce domain-based phenotypic ontologies in addition to GO. |
format | Text |
id | pubmed-3013712 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2011 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-30137122011-01-03 SUPERFAMILY 1.75 including a domain-centric gene ontology method de Lima Morais, David A. Fang, Hai Rackham, Owen J. L. Wilson, Derek Pethica, Ralph Chothia, Cyrus Gough, Julian Nucleic Acids Res Articles The SUPERFAMILY resource provides protein domain assignments at the structural classification of protein (SCOP) superfamily level for over 1400 completely sequenced genomes, over 120 metagenomes and other gene collections such as UniProt. All models and assignments are available to browse and download at http://supfam.org. A new hidden Markov model library based on SCOP 1.75 has been created and a previously ignored class of SCOP, coiled coils, is now included. Our scoring component now uses HMMER3, which is in orders of magnitude faster and produces superior results. A cloud-based pipeline was implemented and is publicly available at Amazon web services elastic computer cloud. The SUPERFAMILY reference tree of life has been improved allowing the user to highlight a chosen superfamily, family or domain architecture on the tree of life. The most significant advance in SUPERFAMILY is that now it contains a domain-based gene ontology (GO) at the superfamily and family levels. A new methodology was developed to ensure a high quality GO annotation. The new methodology is general purpose and has been used to produce domain-based phenotypic ontologies in addition to GO. Oxford University Press 2011-01 2010-11-08 /pmc/articles/PMC3013712/ /pubmed/21062816 http://dx.doi.org/10.1093/nar/gkq1130 Text en © The Author(s) 2010. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/2.5 This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Articles de Lima Morais, David A. Fang, Hai Rackham, Owen J. L. Wilson, Derek Pethica, Ralph Chothia, Cyrus Gough, Julian SUPERFAMILY 1.75 including a domain-centric gene ontology method |
title | SUPERFAMILY 1.75 including a domain-centric gene ontology method |
title_full | SUPERFAMILY 1.75 including a domain-centric gene ontology method |
title_fullStr | SUPERFAMILY 1.75 including a domain-centric gene ontology method |
title_full_unstemmed | SUPERFAMILY 1.75 including a domain-centric gene ontology method |
title_short | SUPERFAMILY 1.75 including a domain-centric gene ontology method |
title_sort | superfamily 1.75 including a domain-centric gene ontology method |
topic | Articles |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013712/ https://www.ncbi.nlm.nih.gov/pubmed/21062816 http://dx.doi.org/10.1093/nar/gkq1130 |
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