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Bioinformatics Advance Access published online on September 25, 2007
Bioinformatics, doi:10.1093/bioinformatics/btm468
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© The Author (2007). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

CREx: Inferring Genomic Rearrangements Based on Common Intervals

Matthias Bernt a,*, Daniel Merkle a, Kai Ramsch a, Guido Fritzsch b,c, Marleen Perseke d, Detlef Bernhard d, Martin Schlegel d, Peter Stadler b,c,e,f,g and Martin Middendorf a

aParallel Computing and Complex Systems Group, bBioinformatics Group, Dept. of Computer Science, cInterdisciplinary Center for Bioinformatics, dInstitute of Biology II, University of Leipzig,Germany; eFraunhofer Institute IZI, Leipzig, Germany; fDept. of Theoretical Chemistry, University of Vienna, Austria; gThe Santa Fe Institute;

*To whom correspondence should be addressed. Dr. Daniel Merkle, E-mail: merkle{at}informatik.uni-leipzig.de


  Abstract

Summary: We present the web-based program CREx for heuristically determining pairwise rearrangement events in unichromosomal genomes. CREx considers transpositions, reverse transpositions, reversals, and tandem-duplication-random-loss (TDRL) events. It supports the user in finding parsimonious rearrangement scenarios given a phylogenetic hypothesis. CREx is based on common intervals, which reflect genes that appear consecutively in several of the input gene orders.

Availability: CREx is freely available at http://pacosy.informatik.unileipzig.de/crex

Associate Editor: Prof. Keith Crandall

Received on June 27, 2007; revised on September 7, 2007; accepted on September 7, 2007

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