automatic selection of representative proteins for bacterial phylogeny自动选择代表蛋白质的细菌的发展史.pdfVIP

BMC Evolutionary Biology BioMed Central Research article Open Access Automatic selection of representative proteins for bacterial phylogeny Marshall Bern* and David Goldberg Address: Palo Alto Research Center, 3333 Coyote Hill Road, Palo Alto, CA 94304, USA Email: Marshall Bern* - bern@; David Goldberg - goldberg@ * Corresponding author Published: 31 May 2005 Received: 02 November 2004 Accepted: 31 May 2005 BMC Evolutionary Biology 2005, 5:34 doi:10.1186/1471-2148-5-34 This article is available from: /1471-2148/5/34 © 2005 Bern and Goldberg; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: Although there are now about 200 complete bacterial genomes in GenBank, deep bacterial phylogeny remains a difficult problem, due to confounding horizontal gene transfers and other phylogenetic noise. Previous methods have relied primarily upon biological intuition or manual curation for choosing genomic sequences unlikely to be horizontally transferred, and have given inconsistent phylogenies with poor bootstrap confidence. Results: We describe an algorithm that automatically picks representative protein families from entire genomes for use as phylogenetic characters. A representative protein family is one that, taken alon