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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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: | https://repository.cshl.edu/id/eprint/15293 |
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