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Bioinformatics Advance Access originally published online on January 30, 2008
Bioinformatics 2008 24(6):863-865; 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 prokaryotic 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, 1050 Bruxelles, Belgium

*To whom correspondence should be addressed.


  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: Softare is available at http://aclame.ulb.ac.be/prophinder

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

Supplementary information: Supplementary data is available on http://aclame.ulb.ac.be/Tools/Prophinder/evaluations_table.html.

Associate Editor: Alfonso Valencia

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

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