Self-overlapping Occurrences and Knuth-Morris-Pratt Algorithm for Weighted Matching
Position Weight Matrices are broadly used probabilistic motif models. In this paper, we address the problem of identifying and characterizing potential overlaps between occurrences of such a motif. It has useful applications to the statistics of the number of occurrences, and to weighted pattern matching with an extension of the well-known Knuth-Morris-Pratt algorithm.
KeywordsPattern Match Score Threshold Position Weight Matrix Position Weight Matrice Shift Rule
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- 1.Mount, S.: A catalogue of splice junction sequences. Nucleic Acids Research 10, 459–472 (1982)Google Scholar
- 5.Knuth, D., Morris Jr., J., Pratt, V.: Fast pattern matching in strings. SIAM Journal on Computing (1977)Google Scholar
- 7.Aho, A., Corasick, M.: Efficient string matching: an aid to bibliographic search. Communications of the ACM (1975)Google Scholar
- 8.Sandelin, A., Alkema, W., Engström, P., Wasserman, W.: Jaspar: an open-access database for eukaryotic transcription factor binding profiles. Nucleic Acids Research (2004)Google Scholar
- 10.Staden, R.: Methods for calculating the probabilities of finding patterns in sequences. Comput. Appl. Biosci. 5, 89–96 (1989)Google Scholar
- 11.Touzet, H., Varré, J.S.: Efficient and accurate p-value computation for position weight matrices. Algorithms for Molecular Biology 2 (2007)Google Scholar
- 13.Beckstette, M., Homann, R., Giegerich, R., Kurtz, S.: Fast index based algorithms and software for matching position specific scoring matrices. BMC Bioinformatics (2006)Google Scholar