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Bioinformatics Advance Access published online on April 6, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl139
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© The Author (2006). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received February 3, 2006
Revised April 4, 2006
Accepted April 4, 2006

Article

GRAST: a new way of genome reduction analysis using comparative genomics

Christina Toft 1 and Mario A. Fares 1 *

1 Molecular Evolution and Bioinformatics Laboratory, Department of Biology, National University of Ireland, Maynooth

* To whom correspondence should be addressed.
Mario A. Fares, E-mail: mario.fares{at}nuim.ie


  Abstract

Motivation: Establishment of intra-cellular life involved a profound re-configuration of the genetic characteristics of bacteria, including genome reduction and rearrangements. Understanding the mechanisms underlying these phenomena will shed light on the genome rearrangements essential for the development of an intra-cellular lifestyle. Comparison of genomes with differences in their sizes poses statistical as well as computational problems. Little efforts have been made to develop flexible computational tools with which to analyse genome reduction and rearrangements.

Results: Investigation of genome reduction and rearrangements in endosymbionts using a novel computational tool (GRAST) identified gathering of genes with similar functions. Conserved clusters of functionally related genes (CGSCs) were detected. Heterogeneous gene and gene cluster non-functionalisation/loss are identified between genome regions, functional gene categories and during evolution. Results show that gene non-functionalisation has accelerated during the last 50 MY of Buchnera's evolution while CGSCs have been static.

Availability: Software is available at http://biology.nuim.ie/staff/mfmolecevolandbioinf.shtml.

Associate Editor: Dmitrij Frishman
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