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B2G-FAR, a species-centered GO annotation repository
Motivation: Functional genomics research has expanded enormously in the last decade thanks to the cost reduction in high-throughput technologies and the development of computational tools that generate, standardize and share information on gene and protein function such as the Gene Ontology (GO). Ne...
Autores principales: | , , , , , , , , |
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Formato: | Texto |
Lenguaje: | English |
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Oxford University Press
2011
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3065692/ https://www.ncbi.nlm.nih.gov/pubmed/21335611 http://dx.doi.org/10.1093/bioinformatics/btr059 |
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author | Götz, Stefan Arnold, Roland Sebastián-León, Patricia Martín-Rodríguez, Samuel Tischler, Patrick Jehl, Marc-André Dopazo, Joaquín Rattei, Thomas Conesa, Ana |
author_facet | Götz, Stefan Arnold, Roland Sebastián-León, Patricia Martín-Rodríguez, Samuel Tischler, Patrick Jehl, Marc-André Dopazo, Joaquín Rattei, Thomas Conesa, Ana |
author_sort | Götz, Stefan |
collection | PubMed |
description | Motivation: Functional genomics research has expanded enormously in the last decade thanks to the cost reduction in high-throughput technologies and the development of computational tools that generate, standardize and share information on gene and protein function such as the Gene Ontology (GO). Nevertheless, many biologists, especially working with non-model organisms, still suffer from non-existing or low-coverage functional annotation, or simply struggle retrieving, summarizing and querying these data. Results: The Blast2GO Functional Annotation Repository (B2G-FAR) is a bioinformatics resource envisaged to provide functional information for otherwise uncharacterized sequence data and offers data mining tools to analyze a larger repertoire of species than currently available. This new annotation resource has been created by applying the Blast2GO functional annotation engine in a strongly high-throughput manner to the entire space of public available sequences. The resulting repository contains GO term predictions for over 13.2 million non-redundant protein sequences based on BLAST search alignments from the SIMAP database. We generated GO annotation for approximately 150 000 different taxa making available 2000 species with the highest coverage through B2G-FAR. A second section within B2G-FAR holds functional annotations for 17 non-model organism Affymetrix GeneChips. Conclusions: B2G-FAR provides easy access to exhaustive functional annotation for 2000 species offering a good balance between quality and quantity, thereby supporting functional genomics research especially in the case of non-model organisms. Availability: The annotation resource is available at http://www.b2gfar.org. Contact: aconesa@cipf.es; sgoetz@cipf.es Supplementary information: Supplementary data are available at Bioinformatics online. |
format | Text |
id | pubmed-3065692 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2011 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-30656922011-03-30 B2G-FAR, a species-centered GO annotation repository Götz, Stefan Arnold, Roland Sebastián-León, Patricia Martín-Rodríguez, Samuel Tischler, Patrick Jehl, Marc-André Dopazo, Joaquín Rattei, Thomas Conesa, Ana Bioinformatics Original Papers Motivation: Functional genomics research has expanded enormously in the last decade thanks to the cost reduction in high-throughput technologies and the development of computational tools that generate, standardize and share information on gene and protein function such as the Gene Ontology (GO). Nevertheless, many biologists, especially working with non-model organisms, still suffer from non-existing or low-coverage functional annotation, or simply struggle retrieving, summarizing and querying these data. Results: The Blast2GO Functional Annotation Repository (B2G-FAR) is a bioinformatics resource envisaged to provide functional information for otherwise uncharacterized sequence data and offers data mining tools to analyze a larger repertoire of species than currently available. This new annotation resource has been created by applying the Blast2GO functional annotation engine in a strongly high-throughput manner to the entire space of public available sequences. The resulting repository contains GO term predictions for over 13.2 million non-redundant protein sequences based on BLAST search alignments from the SIMAP database. We generated GO annotation for approximately 150 000 different taxa making available 2000 species with the highest coverage through B2G-FAR. A second section within B2G-FAR holds functional annotations for 17 non-model organism Affymetrix GeneChips. Conclusions: B2G-FAR provides easy access to exhaustive functional annotation for 2000 species offering a good balance between quality and quantity, thereby supporting functional genomics research especially in the case of non-model organisms. Availability: The annotation resource is available at http://www.b2gfar.org. Contact: aconesa@cipf.es; sgoetz@cipf.es Supplementary information: Supplementary data are available at Bioinformatics online. Oxford University Press 2011-04-01 2011-02-18 /pmc/articles/PMC3065692/ /pubmed/21335611 http://dx.doi.org/10.1093/bioinformatics/btr059 Text en © The Author(s) 2011. 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 | Original Papers Götz, Stefan Arnold, Roland Sebastián-León, Patricia Martín-Rodríguez, Samuel Tischler, Patrick Jehl, Marc-André Dopazo, Joaquín Rattei, Thomas Conesa, Ana B2G-FAR, a species-centered GO annotation repository |
title | B2G-FAR, a species-centered GO annotation repository |
title_full | B2G-FAR, a species-centered GO annotation repository |
title_fullStr | B2G-FAR, a species-centered GO annotation repository |
title_full_unstemmed | B2G-FAR, a species-centered GO annotation repository |
title_short | B2G-FAR, a species-centered GO annotation repository |
title_sort | b2g-far, a species-centered go annotation repository |
topic | Original Papers |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3065692/ https://www.ncbi.nlm.nih.gov/pubmed/21335611 http://dx.doi.org/10.1093/bioinformatics/btr059 |
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