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Bioinformatics Advance Access originally published online on September 25, 2007
Bioinformatics 2007 23(21):2957-2958; 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 1,*, Daniel Merkle 1, Kai Ramsch 1, Guido Fritzsch 2,3, Marleen Perseke 4, Detlef Bernhard 4, Martin Schlegel 4, Peter F. Stadler 2,3,5,6,7 and Martin Middendorf 1

1Parallel Computing and Complex Systems Group, 2Bioinformatics Group, Department of Computer Science, 3Interdisciplinary Center for Bioinformatics, 4Institute of Biology II, University of Leipzig, 5Fraunhofer Institute IZI, Leipzig, Germany, 6Department of Theoretical Chemistry, University of Vienna, Austria and 7Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA

*To whom correspondence should be addressed.


  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.uni-leipzig.de/crex

Contact: merkle{at}informatik.uni-leipzig.de

Associate Editor: Keith Crandall

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

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