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Updated: Aug 17, 2026

An Integrated Approach for Microprotein Identification and Sequence Analysis
Published on: July 12, 2022
Computing the P-value of the information content from an alignment of multiple sequences
Niranjan Nagarajan1, Neil Jones, Uri Keich
1Computer Science Department 4130 Upson Hall Cornell University Ithaca, NY 14853, USA.
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
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