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Bioinformatics Advance Access originally published online on October 17, 2007
Bioinformatics 2008 24(1):127-128; doi:10.1093/bioinformatics/btm449
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© The Author 2007. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

i-ADHoRe 2.0: an improved tool to detect degenerated genomic homology using genomic profiles

Cedric Simillion 1, Koen Janssens 2, Lieven Sterck 3,4 and Yves Van de Peer 3,4,*

1Institute for Cell and Molecular Biosciences (ICaMB), Newcastle University, Newcastle-upon-Tyne, UK, 2Departement Industriële Wetenschappen BME-CTL, Hogeschool Gent, B-9000 Ghent, 3Department of Plant Systems Biology, VIB and 4Bioinformatics and Evolutionary Genomics, Department of Molecular Genetics, Ghent University, B-9052 Ghent, Belgium

*To whom correspondence should be addressed.


  Abstract

Summary: i-ADHoRe is a software tool that combines gene content and gene order information of homologous genomic segments into profiles to detect highly degenerated homology relations within and between genomes. The new version offers, besides a significant increase in performance, several optimizations to the algorithm, most importantly to the profile alignment routine. As a result, the annotations of multiple genomes, or parts thereof, can be fed simultaneously into the program, after which it will report all regions of homology, both within and between genomes.

Availability: The i-ADHoRe 2.0 package contains the C++ source code for the main program as well as various Perl scripts and a fully documented Perl API to facilitate post-processing. The software runs on any Linux- or -UNIX based platform. The package is freely available for academic users and can be downloaded from http://bioinformatics.psb.ugent.be/

Contact: yves.vandepeer{at}psb.ugent.be

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Alex Bateman

Received on May 28, 2007; revised on August 18, 2007; accepted on August 24, 2007

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