Skip Navigation

Nucleic Acids Research 2004 32(21):6347-6357; doi:10.1093/nar/gkh935
This Article
Right arrow Full Text Freely available
Right arrow Print PDF (741K) Freely available
Right arrow Supplementary Material
Right arrow Supplementary Material
Right arrow Supplementary Material
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 (6)
Right arrowRequest Permissions
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Zheng, Y.
Right arrow Articles by Kasif, S.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Zheng, Y.
Right arrow Articles by Kasif, S.
Related Collections
Right arrow Genomics
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Published online 2 December 2004

Nucleic Acids Research, Vol. 32 No. 21 © Oxford University Press 2004; all rights reserved

Identification of genes with fast-evolving regions in microbial genomes

Yu Zheng1, Richard J. Roberts3 and Simon Kasif1,2,*

1 Bioinformatics Graduate Program and 2 Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA and 3 New England Biolabs, Beverly, MA 01915, USA

* To whom correspondence should be addressed. Tel: +1 617 358 1845; Fax: +1 617 353 6766; Email: kasif{at}bu.edu
Present address: Yu Zheng, New England Biolabs, 32 Tozer Road, Beverly, MA 01915, USA

Received August 30, 2004; Revised and Accepted October 25, 2004

Complete sequences of multiple strains of the same microbial species provide an invaluable source for studying the evolutionary dynamics between orthologous genes over a relatively short time scale. Usually the intensity of the selection pressure is inferred from a comparison between the nonsynonymous substitution rate and the synonymous substitution rate. In this paper, we propose an alternative method for detecting genes with one or more fast-evolving regions from pairwise comparisons of orthologous genes. Our method looks for regions with overrepresented nonsynonymous mutations along the alignment, and requires a higher nonsynonymous evolution rate in those regions than the neutral evolution rate. It identifies gene targets under intensive selection pressure that are not detected from the conventional rate comparison analysis. For those identified genes with known annotations, most of them have a clear role in processes such as bacterial defense and host–pathogen interactions. Gene sets reported from our method provide a measure of the phenotypic divergence between two closely related genomes.


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
C. H. Lin, G. Bourque, and P. Tan
A Comparative Synteny Map of Burkholderia Species Links Large-Scale Genome Rearrangements to Fine-Scale Nucleotide Variation in Prokaryotes
Mol. Biol. Evol., March 1, 2008; 25(3): 549 - 558.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
P. Escobar-Paramo, S. Ghosh, and J. DiRuggiero
Evidence for Genetic Drift in the Diversification of a Geographically Isolated Population of the Hyperthermophilic Archaeon Pyrococcus
Mol. Biol. Evol., November 1, 2005; 22(11): 2297 - 2303.
[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.