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Bioinformatics 2005 21(Suppl 1):i311-i318; doi:10.1093/bioinformatics/bti1044
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

Computing the P-value of the information content from an alignment of multiple sequences

Niranjan Nagarajan 1, Neil Jones 2 and Uri Keich 1,*

1Computer Science Department 4130 Upson Hall Cornell University Ithaca, NY 14853, USA
2Department of Computer Science and Engineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA

*To whom correspondence should be addressed.

Motivation: The efficient and accurate computation of P-values is an essential requirement for motif-finding and alignment tools. We show that the approximation algorithms used in two popular motif-finding programs, MEME and Consensus, can fail to accurately compute the P-value.

Results: We present two new algorithms: one for the evaluation of the P-values of a range of motif scores, and a faster one for the evaluation of the P-value of a single motif score. Both exhibit more reliability than existing algorithms, and the latter algorithm is comparable in speed to the fastest existing method.

Availability: The algorithms described in this paper are available from http://www.cs.cornell.edu/~keich

Contact: keich{at}cs.cornell.edu

Received on January 15, 2005; accepted on March 27, 2005

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