Abstract
We consider a string matching problem where the pattern is a template that matches many different strings with various degrees of perfection. The quality of a match is given by a penalty matrix that assigns each pair of characters a score that characterizes how well the characters match. Superfluous characters in the text and superfluous characters in the pattern may also occur and the respective penalties for such gaps in the alignment are also given by the penalty matrix. For a text T of length n, and a template P of length m, we wish to find the best alignment of T with P n, which is the concatenation of n copies of P, (m will typically be much smaller than n). Such an alignment can simply be obtained by solving a dynamic programming problem of size O(n2 m), and ignoring the periodic character of P n. We show that the structure of Pn can be exploited and the problem reduced to essentially solving a dynamic programming of size O(mn). If the complexity of computing gap penalties is O(1), (which is frequently the case), our algorithm runs in O(mn) time. The problem was motivated by a protein structure problem.
Partially supported by NSF grant CCR-8908286
Partially supported by NSF grant CCR-9110255 and the New York State Science and Technology Foundation Center for Advanced Technology
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© 1992 Springer-Verlag Berlin Heidelberg
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Fischetti, V.A., Landau, G.M., Schmidt, J.P., Sellers, P.H. (1992). Identifying periodic occurrences of a template with applications to protein structure. In: Apostolico, A., Crochemore, M., Galil, Z., Manber, U. (eds) Combinatorial Pattern Matching. CPM 1992. Lecture Notes in Computer Science, vol 644. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-56024-6_9
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DOI: https://doi.org/10.1007/3-540-56024-6_9
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