title: Computing the P-value of the information content from an alignment of multiple sequences.
abstract: 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
authors.affiliation: Computer Science Department 4130 Upson Hall Cornell University Ithaca, NY 14853, USA.
authors.forename: Niranjan
authors.initials: N
authors.lastname: Nagarajan
authors.forename: Neil
authors.initials: N
authors.lastname: Jones
authors.forename: Uri
authors.initials: U
authors.lastname: Keich
mesh_terms: 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