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Multi-pattern matching with variable-length wildcards using suffix tree

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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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Acknowledgements

This research is supported by the National Key Research and Development Program of China (Grant No. 2016YFB1000900) and National Natural Science Foundation of China (NSFC) (Grant Nos. 61503116 and 61229301).

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Authors and Affiliations

  1. School of Computer Science and Information Engineering, Hefei University of Technology, Hefei, China

    Na Liu & Xindong Wu

  2. School of General Education, Beifang Minzu University, Yinchuan, China

    Na Liu

  3. Department of Computer Science and Technology, Hefei Normal University, Hefei, China

    Fei Xie

  4. School of Computing and Informatics, University of Louisiana, Lafayette, LA, USA

    Xindong Wu

Authors
  1. Na Liu
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  2. Fei Xie
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  3. Xindong Wu
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Correspondence to Na Liu.

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Liu, N., Xie, F. & Wu, X. Multi-pattern matching with variable-length wildcards using suffix tree. Pattern Anal Applic 21, 1151–1165 (2018). https://doi.org/10.1007/s10044-018-0733-0

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