tailieunhanh - a database of protein functional linkages derived from coevolution

Published: 16 April 2004 Genome Biology 2004, 5:R35 The electronic version of this article is the complete one and can be found online at Received: 7 January 2004 Revised: 23 February 2004 Accepted: 4 March 2004 reports © 2004 Bowers et al.; licensee BioMed Central Ltd. This is an Open Access article: verbatim copying and redistribution of this article are permitted in all media for any purpose, provided this notice is preserved along with the article's original URL | Software Open Access Prolinks a database of protein functional linkages derived from coevolution Peter M Bowers Matteo Pellegrini Mike J Thompson Joe Fierro Todd O Yeates and David Eisenberg Addresses Institute for Genomics and Proteomics University of California Los Angeles CA 90095 USA. 454 Corporation Branford CT 06405 USA. Correspondence David Eisenberg. E-mail david@ Published 16 April 2004 Genome Biology 2004 5 R35 The electronic version of this article is the complete one and can be found online at http 2004 5A5 R35 Received 7 January 2004 Revised 23 February 2004 Accepted 4 March 2004 2004 Bowers et al. licensee BioMed Central Ltd. This is an Open Access article verbatim copying and redistribution of this article are permitted in all media for any purpose provided this notice is preserved along with the article s original URL. Abstract The advent of whole-genome sequencing has led to methods that infer protein function and linkages. We have combined four such algorithms phylogenetic profile Rosetta Stone gene neighbor and gene cluster in a single database - Prolinks - that spans 83 organisms and includes 10 million high-confidence links. The Proteome Navigator tool allows users to browse predicted linkage networks interactively providing accompanying annotation from public databases. The Prolinks database and the Proteome Navigator tool are available for use online at http pronav. Rationale Genome sequencing has allowed scientists to identify most of the genes encoded in each organism. The function of many typically 50 of translated proteins can be inferred from sequence comparison with previously characterized sequences. However the assignment of function by homology gives only a partial understanding of a protein s role within a cell. A more complete understanding of protein function requires the identification of interacting partners interacting subunits if the protein is a component of a molecular .