Computing exact P-values for DNA motifs

Zhang, J., Jiang, B., Li, M., Tromp, J., Zhang, X. G., Zhang, M. Q. (March 2007) Computing exact P-values for DNA motifs. Bioinformatics, 23 (5). pp. 531-537. ISSN 1367-4803

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URL: https://www.ncbi.nlm.nih.gov/pubmed/17237046
DOI: 10.1093/bioinformatics/btl662

Abstract

Motivation: Many heuristic algorithms have been designed to approximate P-values of DNA motifs described by position weight matrices, for evaluating their statistical significance. They often significantly deviate from the true P-value by orders of magnitude. Exact P-value computation is needed for ranking the motifs. Furthermore, surprisingly, the complexity of the problem is unknown. Results: We show the problem to be NP-hard, and present MotifRank, software based on dynamic programming, to calculate exact P-values of motifs. We define the exact P-value on a general and more precise model. Asymptotically, MotifRank is faster than the best exact P-value computing algorithm, and is in fact practical. Our experiments clearly demonstrate that MotifRank significantly improves the accuracy of existing approximation algorithms.

Item Type: Paper
Uncontrolled Keywords: PROBABILITIES REPRESENTATION COMPUTATION SEQUENCES PATTERNS SEARCH
Subjects: bioinformatics > quantitative biology
bioinformatics > genomics and proteomics > computers > computer software
CSHL Authors:
Communities: CSHL labs > Zhang lab
Depositing User: CSHL Librarian
Date: March 2007
Date Deposited: 30 Aug 2011 13:10
Last Modified: 11 Apr 2018 15:55
Related URLs:
URI: http://repository.cshl.edu/id/eprint/15293

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