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


BACKGROUND
The algorithms described in this paper are available from http://www.cs.cornell.edu/~keich
Nagarajan
Niranjan
N
Computer Science Department 4130 Upson Hall Cornell University Ithaca, NY 14853, USA.
Jones
Neil
N
Keich
Uri
U
D000465:Algorithms; D020816:Amino Acid Motifs; D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D019277:Entropy; D015233:Models, Statistical; D015203:Reproducibility of Results; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein; D013997:Time Factors