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

  • Authors:

  • Niranjan Nagarajan;Neil Jones;Uri Keich

  • Affiliations:

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

  • Venue:
  • Bioinformatics
  • Year:
  • 2005

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Abstract

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@cs.cornell.edu