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Bioinformatics Advance Access published online on April 26, 2007
Bioinformatics, 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. Falk Hüffneri, E-mail: hueffner{at}minet.uni-jena.de


  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.

Associate Editor: Prof. Anna Tramontano

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

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