Skip Navigation


Bioinformatics Advance Access originally published online on May 27, 2004
Bioinformatics 2005 21(10):2329-2335; doi:10.1093/bioinformatics/bth324
This Article
Right arrow Full Text Freely available
Right arrow FREE Full Text (Print PDF) Freely available
Right arrow All Versions of this Article:
21/10/2329    most recent
bth324v1
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (19)
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Henz, S. R.
Right arrow Articles by Schuster, S. C.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Henz, S. R.
Right arrow Articles by Schuster, S. C.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author 2004. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

Whole-genome prokaryotic phylogeny

Stefan R. Henz 1, Daniel H. Huson 1,*, Alexander F. Auch 1, Kay Nieselt-Struwe 1 and Stephan C. Schuster 2

1Center for Bioinformatics Tübingen (ZBIT) Sand 14, Tübingen 72076, Germany
2Max-Planck-Institute for Development Biology Spemannstrasse 35, Tübingen, 72076, Germany

*To whom correspondence should be addressed.

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.

Contact: huson{at}informatik.uni-tuebingen.de


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Mol Biol EvolHome page
M. Irimia, I. Maeso, D. Penny, J. Garcia-Fernandez, and S. W. Roy
Rare Coding Sequence Changes are Consistent with Ecdysozoa, not Coelomata
Mol. Biol. Evol., August 1, 2007; 24(8): 1604 - 1607.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
G. C. Gibb, O. Kardailsky, R. T. Kimball, E. L. Braun, and D. Penny
Mitochondrial Genomes and Avian Phylogeny: Complex Characters and Resolvability without Explosive Radiations
Mol. Biol. Evol., January 1, 2007; 24(1): 269 - 280.
[Abstract] [Full Text] [PDF]

Home page
 MicrobiologyHome page
C. Canchaya, M. J. Claesson, G. F. Fitzgerald, D. van Sinderen, and P. W. O'Toole
Diversity of the genus Lactobacillus revealed by comparative genomics of five species.
Microbiology, November 1, 2006; 152(Pt 11): 3185 - 3196.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
X. Xia, H. Wang, Z. Xie, M. Carullo, H. Huang, and D. Hickey
Cytosine Usage Modulates the Correlation between CDS Length and CG Content in Prokaryotic Genomes
Mol. Biol. Evol., July 1, 2006; 23(7): 1450 - 1454.
[Abstract] [Full Text] [PDF]

Home page
 Brief BioinformHome page
T. G. Lilburn, S. H. Harrison, J. R. Cole, and G. M. Garrity
Computational aspects of systematic biology
Brief Bioinform, June 1, 2006; 7(2): 186 - 195.
[Abstract] [Full Text] [PDF]


Disclaimer:
Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.