Sun, 20 Jul 2008 13:45:32 BST CiteULike: jyuh Talon http://www.citeulike.org/user/jyuh/author/Talon CiteULike.org en-gb Copyright © 2004-2008 citeulike.org http://www.citeulike.org/user/jyuh/article/2733895 <i>Nucl. Acids Res. (29 April 2008), gkn176.</i><br /><br />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. 10.1093/nar/gkn176 High-throughput functional annotation and data mining with the Blast2GO suite Stefan Gotz Juan Garcia-Gomez Javier Terol Tim Williams Shivashankar Nagaraj Maria Nueda Montserrat Robles Manuel Talon Joaquin Dopazo Ana Conesa doi:10.1093/nar/gkn176 Nucl. Acids Res. (29 April 2008), gkn176. 2008-04-29T11:39:18-00:00 2008 Nucl. Acids Res. gkn176 blast ontology http://www.citeulike.org/user/jyuh/article/1234112 <i>Stud Health Technol Inform, Vol. 120 (2006), pp. 194-204.</i><br /><br />The vast amount in complexity of data generated in Genomic Research implies that new dedicated and powerful computational tools need to be developed to meet their analysis requirements. Blast2GO (B2G) is a bioinformatics tool for Gene Ontology-based DNA or protein sequence annotation and function-based data mining. The application has been developed with the aim of affering an easy-to-use tool for functional genomics research. Typical B2G users are middle size genomics labs carrying out sequencing, ETS and microarray projects, handling datasets up to several thousand sequences. In the current version of B2G. The power and analytical potential of both annotation and function data-mining is somehow restricted to the computational power behind each particular installation. In order to be able to offer the possibility of an enhanced computational capacity within this bioinformatics application, a Grid component is being developed. A prototype has been conceived for the particular problem of speeding up the Blast searches to obtain fast results for large datasets. Many efforts have been done in the literature concerning the speeding up of Blast searches, but few of them deal with the use of large heterogeneous production Grid Infrastructures. These are the infrastructures that could reach the largest number of resources and the best load balancing for data access. The Grid Service under development will analyse requests based on the number of sequences, splitting them accordingly to the available resources. Lower-level computation will be performed through MPIBLAST. The software architecture is based on the WSRF standard. Blast2GO goes grid: developing a grid-enabled prototype for functional genomics analysis. G Aparicio S Götz A Conesa D Segrelles I Blanquer JM García V Hernandez M Robles M Talon Stud Health Technol Inform, Vol. 120 (2006), pp. 194-204. 2007-04-18T14:03:22-00:00 2006 Stud Health Technol Inform 0926-9630 120 194 204 no-tag