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Bioinformatics Advance Access first published online on August 27, 2007
This version published online on October 17, 2007
Bioinformatics, doi:10.1093/bioinformatics/btm405
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© The Author (2007). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Identification of compositionally distinct regions in genomes using the centroid method

Issaac Rajan 1, Sarang Aravamuthan 2 and Sharmila S. Mande 1,*

1Life Sciences Research, 2e-Security R&D, Advanced Technology Centre, Tata Consultancy Services, Hyderabad 500 081, Andhra Pradesh, India

*To whom correspondence should be addressed. Dr. Sharmila S. Mande, E-mail: sharmila{at}atc.tcs.com


  Abstract

Motivation: It is known that most genomic regions of special interest, e.g., horizontally acquired sequences, genomic islands, etc., have distinct word (m-mer) compositions. Most of the earlier work along this direction, addressed di- and tri-nucleotide compositions only. Thus there is a need for newer We present an approaches that can be applied to analyze compositions of any given word size. The method presented here, called the centroid approach, can reveal compositionally distinct regions in genomic sequences, for any given word size.

Results: We applied our method to 50 bacterial genomes and demonstrated its ability to identify embedded sequences of varying lengths from distantly related organisms. We also investigated the genetic makeup of the regions identified as compositionally distinct by our method, for four organisms from our dataset. Pathogenicity island components and genes encoding strain-specific proteins are all frequently seen to be constituents of these regions.

Availability: Program is available on request from the authors.

Contacts: issaacr{at}atc.tcs.com, sarang{at}atc.tcs.com, sharmila{at}atc.tcs.com

Supplementary Information: Supplementary data are available at Bioinformatics online.

Associate Editor: Prof. Burkhard Rost

Received on January 23, 2007; revised on July 16, 2007; accepted on August 6, 2007

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