On the massive string matching problem

In this paper, we discuss an efficient and effective index mechanism to support the matching of massive pattern strings in against a very long target string. It is very important to the next generation sequencing in the biological research. The main idea behind it is to construct an automaton over all the pattern strings, and search the automaton against a BWT-array L created for a target string s to locate all the occurrences of every pattern in s once for all. Experiments have been conducted, which show that our method for this problem is better than the existing approaches.