Nucleic Acids Research Advance Access published online on April 29, 2008
Nucleic Acids Research, doi:10.1093/nar/gkn176
Computational Biology |
High-throughput functional annotation and data mining with the Blast2GO suite
1Bioinformatics Department, Centro de Investigación Principe Felipe (CIPF), Valencia, 2Center for Biomedical Research on Rare Diseases (CIBERER), Valencia, 3Biomedical Informatics Group, IBIME-ITACA, Universidad Politécnica de Valencia, Valencia, 4Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, Spain, 5School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK, 6Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, Australia, 7Departamento de Estadística e Investigación Operativa, Universidad de Alicante, Alicante and 8Functional Genomics Node (National Institute for Bioinformatics, INB), Valencia, Spain
*To whom correspondence should be addressed. Tel: +34 96 32 89 680; Fax: +34 96 32 89 574; Email: aconesa{at}cipf.es
Received November 9, 2007. Revised March 25, 2008. Accepted March 26, 2008.
Functional genomics technologies have been widely adopted in the biological research of both model and non-model species. An efficient functional annotation of DNA or protein sequences is a major requirement for the successful application of these approaches as functional information on gene products is often the key to the interpretation of experimental results. Therefore, there is an increasing need for bioinformatics resources which are able to cope with large amount of sequence data, produce valuable annotation results and are easily accessible to laboratories where functional genomics projects are being undertaken. We present the Blast2GO suite as an integrated and biologist-oriented solution for the high-throughput and automatic functional annotation of DNA or protein sequences based on the Gene Ontology vocabulary. The most outstanding Blast2GO features are: (i) the combination of various annotation strategies and tools controlling type and intensity of annotation, (ii) the numerous graphical features such as the interactive GO-graph visualization for gene-set function profiling or descriptive charts, (iii) the general sequence management features and (iv) high-throughput capabilities. We used the Blast2GO framework to carry out a detailed analysis of annotation behaviour through homology transfer and its impact in functional genomics research. Our aim is to offer biologists useful information to take into account when addressing the task of functionally characterizing their sequence data.