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Bioinformatics Advance Access published online on January 30, 2008
Bioinformatics, doi:10.1093/bioinformatics/btn043
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© The Author (2008). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Prophinder: a computational tool for prophage prediction in pro-karyotic genomes.

Gipsi Lima-Mendez *, Jacques van Helden , Ariane Toussaint and Raphaël Leplae

Laboratoire de Bioinformatique des Génomes et des Réseaux (BiGRe), Université Libre de Bruxelles, Campus Plaine - CP 263, Boulevard du Triomphe, 1050 Bruxelles, Belgium.

*To whom correspondence should be addressed. Mrs. Gipsi Lima-Mendez, E-mail: gipsi{at}scmbb.ulb.ac.be, raphael{at}scmbb.ulb.ac.be


  Abstract

Summary: Prophinder is a prophage prediction tool coupled with a prediction database, a web server and web service. Predicted prophages will help to fill the gaps in the current sparse phage sequence space, which should cover an estimated 100 million species. Systematic and reliable predictions will enable further studies of prophages contribution to the bacteriophage gene pool and to better understand gene shuffling between prophages and phages infecting the same host.

Availability: http://aclame.ulb.ac.be/prophinder.

Contact: gipsi{at}scmbb.ulb.ac.be

Supplementary information: http://aclame.ulb.ac.be/Tools/Prophinder/evaluations_table.html.

Associate Editor: Prof. Alfonso Valencia

Received on December 10, 2007; revised on January 8, 2008; accepted on January 26, 2008

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