Abstract
Multi-pattern matching with variable-length wildcards is an interesting and important problem in bioinformatics, information retrieval and other domains. Most of the previously developed multi-pattern matching methods, such as famous Aho–Corasick and Wu–Manber algorithms, aimed to solve some classical string matching problems. However, these algorithms are not efficient for patterns with flexible wildcards or do-not-care characters. In this paper, we propose two efficient algorithms for multi-pattern matching with variable-length wildcards based on suffix tree, called MMST-L and MMST-S, according to the length of exact characters in a pattern. Experimental results show that the two MMST algorithms, in most cases, outperform other various versions of comparing algorithms.
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