On-line String Matching in Highly Similar DNA Sequences

Abstract

We consider the problem of on-line exact string matching of a pattern in a set of highly similar sequences. This can be useful in cases where indexing the sequences is not feasible. We present a preliminary study by restricting the problem for a specific case where we adapt the classical Morris-Pratt and Knuth-Morris-Pratt algorithms to consider borders with errors. We give an original algorithm for computing borders at Hamming distance 1. We exhibit experimental results showing that our algorithms are much faster than searching for the pattern in each sequences with a very fast on-line exact string matching algorithm.