Approximate regular expression pattern matching with concave gap penalties

Given a sequenceA of lengthM and a regular expressionR of lengthP, an approximate regular expression pattern-matching algorithm computes the score of the optimal alignment betweenA and one of the sequencesB exactly matched byR. An alignment between sequencesA=a₁a₂ ... a_M andB=b₁b₂... b_N is a list of ordered pairs, (i₁,j₁), (i₂j₂), ..., (i_t,j_tt) such that i_k < i_k+1 and j_k < j_k+1. In this case the alignmentaligns symbols a_ik and b_jk, and leaves blocks of unaligned symbols, orgaps, between them. A scoring schemeS associates costs for each aligned symbol pair and each gap. The alignment's score is the sum of the associated costs, and an optimal alignment is one of minimal score. There are a variety of schemes for scoring alignments. In a concave gap penalty scoring schemeS={, w}, a function (a, b) gives the score of each aligned pair of symbolsa andb, and aconcave function w(k) gives the score of a gap of lengthk. A function w is concave if and only if it has the property that, for allk > 1, w(k + 1) –w(k) w(k) –w(k –1). In this paper we present an O(MP(logM + log²P)) algorithm for approximate regular expression matching for an arbitrary and any concavew.This work was supported in part by the National Institute of Health under Grant RO1 LM04960.