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Bioinformatics Advance Access published online on August 7, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl357
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© The Author (2006). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received December 27, 2005
Revised June 23, 2006
Accepted June 24, 2006

Applications note

Branch and bound computation of exact p-values

Gill Bejerano 1 *

1 Center for Biomolecular Science and Engineering, School of Engineering, 1156 High St., University of California, Santa Cruz CA 95064, USA

* To whom correspondence should be addressed.
Gill Bejerano, E-mail: jill{at}soe.ucsc.edu


  Abstract

Summary: P-value computation is often used in bioinformatics to quantify the surprise, or significance, associated with a given observation. An implementation is provided, that computes the exact p-value associated with any observed sample, against a null multinomial distribution, using the likelihood-ratio statistic. The efficient branch and bound code, far exceeding the full enumeration implemented by commercial packages, is especially useful with small sample, sparse data and rare events, common scenarios in bioinformatics, where approximations are often inaccurate and inappropriate. This code base can also be adapted to compute exact p-values of other statistics in diverse sampling scenarios.

Availability: Freely available at http://www.soe.ucsc.edu/~jill/src/.

Associate Editor: Alex Bateman
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