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      Blast2GO: A Comprehensive Suite for Functional Analysis in Plant Genomics

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      Publication date (Electronic):
      Journal: International Journal of Plant Genomics
      Publisher: Hindawi Publishing Corporation

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          Abstract

          Functional annotation of novel sequence data is a primary requirement for the utilization of functional genomics approaches in plant research. In this paper, we describe the Blast2GO suite as a comprehensive bioinformatics tool for functional annotation of sequences and data mining on the resulting annotations, primarily based on the gene ontology (GO) vocabulary. Blast2GO optimizes function transfer from homologous sequences through an elaborate algorithm that considers similarity, the extension of the homology, the database of choice, the GO hierarchy, and the quality of the original annotations. The tool includes numerous functions for the visualization, management, and statistical analysis of annotation results, including gene set enrichment analysis. The application supports InterPro, enzyme codes, KEGG pathways, GO direct acyclic graphs (DAGs), and GOSlim. Blast2GO is a suitable tool for plant genomics research because of its versatility, easy installation, and friendly use.

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          Gene Ontology: tool for the unification of biology

          Michael Ashburner, Catherine A. Ball, Judith Blake … (2002)
          Genomic sequencing has made it clear that a large fraction of the genes specifying the core biological functions are shared by all eukaryotes. Knowledge of the biological role of such shared proteins in one organism can often be transferred to other organisms. The goal of the Gene Ontology Consortium is to produce a dynamic, controlled vocabulary that can be applied to all eukaryotes even as knowledge of gene and protein roles in cells is accumulating and changing. To this end, three independent ontologies accessible on the World-Wide Web (http://www.geneontology.org) are being constructed: biological process, molecular function and cellular component.
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            BRENDA, the enzyme database: updates and major new developments.

            I Schomburg (2004)
            BRENDA (BRaunschweig ENzyme DAtabase) represents a comprehensive collection of enzyme and metabolic information, based on primary literature. The database contains data from at least 83,000 different enzymes from 9800 different organisms, classified in approximately 4200 EC numbers. BRENDA includes biochemical and molecular information on classification and nomenclature, reaction and specificity, functional parameters, occurrence, enzyme structure, application, engineering, stability, disease, isolation and preparation, links and literature references. The data are extracted and evaluated from approximately 46,000 references, which are linked to PubMed as long as the reference is cited in PubMed. In the past year BRENDA has undergone major changes including a large increase in updating speed with >50% of all data updated in 2002 or in the first half of 2003, the development of a new EC-tree browser, a taxonomy-tree browser, a chemical substructure search engine for ligand structure, the development of controlled vocabulary, an ontology for some information fields and a thesaurus for ligand names. The database is accessible free of charge to the academic community at http://www.brenda. uni-koeln.de.
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              GOtcha: a new method for prediction of protein function assessed by the annotation of seven genomes

              David Martin, Matthew Berriman, Geoffrey J. Barton (2004)
              Background The function of a novel gene product is typically predicted by transitive assignment of annotation from similar sequences. We describe a novel method, GOtcha, for predicting gene product function by annotation with Gene Ontology (GO) terms. GOtcha predicts GO term associations with term-specific probability (P-score) measures of confidence. Term-specific probabilities are a novel feature of GOtcha and allow the identification of conflicts or uncertainty in annotation. Results The GOtcha method was applied to the recently sequenced genome for Plasmodium falciparum and six other genomes. GOtcha was compared quantitatively for retrieval of assigned GO terms against direct transitive assignment from the highest scoring annotated BLAST search hit (TOPBLAST). GOtcha exploits information deep into the 'twilight zone' of similarity search matches, making use of much information that is otherwise discarded by more simplistic approaches. At a P-score cutoff of 50%, GOtcha provided 60% better recovery of annotation terms and 20% higher selectivity than annotation with TOPBLAST at an E-value cutoff of 10-4. Conclusions The GOtcha method is a useful tool for genome annotators. It has identified both errors and omissions in the original Plasmodium falciparum annotation and is being adopted by many other genome sequencing projects.
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                Author and article information

                Journal
                Journal ID (nlm-ta): Int J Plant Genomics
                Journal ID (publisher-id): IJPG
                Title: International Journal of Plant Genomics
                Publisher: Hindawi Publishing Corporation
                ISSN (Print): 1687-5370
                ISSN (Electronic): 1687-5389
                Publication date (Print): 2008
                Publication date (Electronic): 30 April 2007
                Volume: 2008
                Electronic Location Identifier: 619832
                Affiliations
                Bioinformatics Department, Centro de Investigación Príncipe Felipe, 4012 Valencia, Spain
                Author notes

                Recommended by Chunguang Du

                Article
                DOI: 10.1155/2008/619832
                PMC ID: 2375974
                PubMed ID: 18483572
                SO-VID: 1fe752f2-a059-446e-bee0-2100b7e8f284
                Copyright © Copyright © 2008 A. Conesa and S. Götz.
                License:

                This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                Date received : 5 October 2007
                Date accepted : 26 November 2007
                Categories
                Subject: Methodology Report

                ScienceOpen disciplines: Plant science & Botany
                Data availability:
                ScienceOpen disciplines: Plant science & Botany

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