Fast Algorithms for Local Similarity Queries in Two Sequences

Abstract

In sequence comparison, finding local similarities in given strings is a very important well-known problem. In this work we introduce two local sequence similarity query problems, and present algorithms for them. Our algorithms use a data structure that supports constant time longest common extension queries. This data structure is created only once, and in time linear in the size of the input strings. After this step all subsequent local similarity queries can be answered very fast. Existing algorithms take significantly more time in answering these queries.