Pattern matching with pair correlation distance

Abstract

In pattern matching with pair correlation distance problem, the goal is to find all occurrences of a pattern P of length m, in a text T of length n, where the distance between them is less than a threshold k. For each text location i, the distance is defined as the number of different kinds of mismatched pairs (α,β), between P and T[i ...i+m]. We present an algorithm with running time of O (min{|∑P|2 n log m, n(m log m) 2/3}) for this problem. Another interesting problem is the one-side pair correlation distance where it is desired to find all occurrences of P where the number of mismatched characters in P is less than k. For this problem, we present an algorithm with running time of O (min{|∑P|2 n log m, n √m log m}). © 2009 Springer Berlin Heidelberg.