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          Institute: MPI für Entwicklungsbiologie     Collection: Abteilungsunabhängige Arbeitsgruppen     Display Documents



ID: 176116.0, MPI für Entwicklungsbiologie / Abteilungsunabhängige Arbeitsgruppen
Whole-genome prokaryotic phylogeny
Authors:Henz, Stefan; Huson, D. H.; Auch, A. F.; Nieselt-Struwe, K.; Schuster, Stephan
Language:English
Date of Publication (YYYY-MM-DD):2004-05
Title of Journal:Bioinformatics
Sequence Number of Article:15166018
Review Status:not specified
Audience:Not Specified
Abstract / Description:Current understanding of the phylogeny of prokaryotes is based on the comparison of the highly conserved small ssu-rRNA subunit and similar regions. Although such molecules have proved to be very useful phylogenetic markers, mutational saturation is a problem, due to their restricted lengths. Now, a growing number of complete prokaryotic genomes are available. This paper addresses the problem of determining a prokaryotic phylogeny utilizing the comparison of complete genomes. We introduce a new strategy, GBDP, "genome blast distance phylogeny", and show that different variants of this approach robustly produce phylogenies that are biologically sound, when applied to 91 prokaryotic genomes. In this approach, first BLAST is used to compare genomes, then a distance matrix is computed, and finally a tree- or network-reconstruction method such as UPGMA, Neighbor-Joining, BioNJ or Neighbor-Net is applied.
External Publication Status:published
Document Type:Article
Affiliations:MPI für Entwicklungsbiologie/Abteilungsunabhängige Arbeitsgruppen
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