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Bioinformatics Advance Access originally published online on April 26, 2007
Bioinformatics 2007 23(13):1708-1709; doi:10.1093/bioinformatics/btm160
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© The Author 2007. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

FASPAD: fast signaling pathway detection

Falk Hüffner *, Sebastian Wernicke and Thomas Zichner

Institut für Informatik, Friedrich-Schiller-Universität Jena, Ernst-Abbe-Platz 2, D-07743 Jena, Germany

*To whom correspondence should be addressed.


  Abstract

Summary: FASPAD is a user-friendly tool that detects candidates for linear signaling pathways in protein interaction networks based on an approach by Scott et al. (Journal of Computational Biology, 2006). Using recent algorithmic insights, it can solve the underlying NP-hard problem quite fast: for protein networks of typical size (several thousand nodes), pathway candidates of length up to 13 proteins can be found within seconds and with a 99.9% probability of optimality. FASPAD graphically displays all candidates that are found; for evaluation and comparison purposes, an overlay of several candidates and the surrounding network context can also be shown.

Availability: FASPAD is available as free software under the GPL license at http://theinf1.informatik.uni-jena.de/faspad/ and runs under Linux and Windows.

Contact: hueffner{at}minet.uni-jena.de

Associate Editor: Anna Tramontano

Received on March 8, 2007; revised on April 16, 2007; accepted on April 19, 2007

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