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Bioinformatics Advance Access published online on May 28, 2008
Bioinformatics, doi:10.1093/bioinformatics/btn249
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© The Author (2008). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

InteroPorc: Automated Inference of Highly Conserved Protein Interaction Networks

Magali Michaut 1,3,*, Samuel Kerrien 3, Luisa Montecchi-Palazzi 3, Franck Chauvat 1, Corinne Cassier-Chauvat 1,2, Jean-Christophe Aude 1 and Pierre Legrain 1

1CEA, IBITECS, Gif sur Yvette, F-91191, France
2CNRS, URA 2096, Gif sur Yvette, F-91191, France
3EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom

*To whom correspondence should be addressed. Magali Michaut, E-mail: michaut.bioinfo{at}gmail.com


  Abstract

Motivation: Protein-protein interaction networks provide insights into the relationships between the proteins of an organism thereby contributing to a better understanding of cellular processes. Nevertheless, large-scale interaction networks are available for only a few model organisms. Thus, interologs are useful for a systematic transfer of protein interaction networks between organisms. However, no standard tool is available so far for that purpose.

Results: In this study, we present an automated prediction tool developed for all sequenced genomes available in Integr8. We also have developed a second method to predict protein-protein interactions in the widely used cyanobacterium Synechocystis. Using these methods, we have constructed a new network of 8,783 inferred interactions for Synechocystis.

Availability: InteroPorc is open-source, downloadable and usable through a web interface at http://biodev.extra.cea.fr/interoporc/

Contact: michaut.bioinfo{at}gmail.com, jean-christophe.aude{at}cea.fr

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Prof. Burkhard Rost

Received on February 18, 2008; revised on May 26, 2008; accepted on May 26, 2008

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