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Bioinformatics Advance Access originally published online on August 7, 2006
Bioinformatics 2006 22(17):2158-2159; 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

Branch and bound computation of exact p-values

Gill Bejerano

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

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/

Contact: jill{at}soe.ucsc.edujill

Received on December 27, 2006; revised on June 23, 2006; accepted on June 24, 2006

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