Abstract
Given a sequence A of length M and a regular expression R of length P, an approximate regular expression pattern matching algorithm computes the score of the best alignment between A and one of the sequences exactly matched by R. There are a variety of schemes for scoring alignments. In a concave gap-penalty scoring scheme, a function δ(a, b) gives the score of each aligned pair of symbols a and b, and a concave function w(k) gives the score of a sequence of unaligned symbols, or gap, of length k. A function w is concave if and only if it has the property that for all k > 1, w(k+ 1)-w(k) <w(k) — w(k−1). In this paper we present an O(MP(log M + log2 P)) algorithm for approximate regular expression matching for an arbitrary δ and any concave w.
This work was supported partially by the National Institute of Health under Grant R01 LM04960 and the Aspen Center for Physics
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© 1992 Springer-Verlag Berlin Heidelberg
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Knight, J.R., Myers, E.W. (1992). Approximate regular expression pattern matching with concave gap penalties. 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_6
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DOI: https://doi.org/10.1007/3-540-56024-6_6
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