PCOGR: Phylogenetic COG ranking as an online tool to judge the specificity of COGs with respect to freely definable groups of organismsReport as inadecuate




PCOGR: Phylogenetic COG ranking as an online tool to judge the specificity of COGs with respect to freely definable groups of organisms - Download this document for free, or read online. Document in PDF available to download.

BMC Bioinformatics

, 5:150

First Online: 15 October 2004Received: 22 July 2004Accepted: 15 October 2004

Abstract

BackgroundThe rapidly increasing number of completely sequenced genomes led to the establishment of the COG-database which, based on sequence homologies, assigns similar proteins from different organisms to clusters of orthologous groups COGs. There are several bioinformatic studies that made use of this database to determine hyperthermophile-specific proteins by searching for COGs containing almost exclusively proteins from hyperthermophilic genomes. However, public software to perform individually definable group-specific searches is not available.

ResultsThe tool described here exactly fills this gap. The software is accessible at http:-www.uni-wh.de-pcogr and is linked to the COG-database. The user can freely define two groups of organisms by selecting for each of the current 66 organisms to belong either to groupA, to the reference groupB or to be ignored by the algorithm. Then, for all COGs a specificity index is calculated with respect to the specificity to groupA, i. e. high scoring COGs contain proteins from the most of groupA organisms while proteins from the most organisms assigned to groupB are absent. In addition to ranking all COGs according to the user defined specificity criteria, a graphical visualization shows the distribution of all COGs by displaying their abundance as a function of their specificity indexes.

ConclusionsThis software allows detecting COGs specific to a predefined group of organisms. All COGs are ranked in the order of their specificity and a graphical visualization allows recognizing i the presence and abundance of such COGs and ii the phylogenetic relationship between groupA- and groupB-organisms. The software also allows detecting putative protein-protein interactions, novel enzymes involved in only partially known biochemical pathways, and alternate enzymes originated by convergent evolution.

Electronic supplementary materialThe online version of this article doi:10.1186-1471-2105-5-150 contains supplementary material, which is available to authorized users.

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Author: Florian Meereis - Michael Kaufmann

Source: https://link.springer.com/







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