All Highest Scoring Paths in Weighted Grid Graphs and Their Application to Finding All Approximate Repeats in Strings

Abstract

Weighted paths in directed grid graphs of dimension (m X n) can be used to model the string edit problem, which consists of obtaining optimal (weighted) alignments between substrings of A, |A|=m, and substrings of B, |B|=n. We build a data structure (in O(mn log m) time) that supports O(log m) time queries about the weight of any of the O(m2n) best paths from the vertices in column 0 of the graph to all other vertices. Using these techniques we present a simple O(n2 log n) time and $\Theta(n^2)$ space algorithm to find all (the locally optimal) approximate tandem (or nontandem) repeats xy within a string of size n. This improves (by a factor of log n) upon several previous algorithms for this problem and is the first algorithm to find all locally optimal repeats. For edit graphs with weights in {0, -1, 1}, a slight modification of our techniques yields an O(n2) algorithm for the cyclic string comparison problem, as compared to O(n2 log n) for the case of general weights.