A novel optimal multi-pattern matching method with wildcards for DNA sequence

Author:

Wang Xinlu12,Saif Ahmed A.F.1,Liu Dayou1,Zhu Yungang1,Benediktsson Jon Atli3

Affiliation:

1. College of Computer Science and Technology, Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin 130012, China

2. College of International Education, Jilin University, Changchun, Jilin 130012, China

3. Faculty of Electrical and Computer Engineering, University of Iceland, Reykjavik 102, Iceland

Abstract

BACKGROUND: DNA sequence alignment is one of the most fundamental and important operation to identify which gene family may contain this sequence, pattern matching for DNA sequence has been a fundamental issue in biomedical engineering, biotechnology and health informatics. OBJECTIVE: To solve this problem, this study proposes an optimal multi pattern matching with wildcards for DNA sequence. METHODS: This proposed method packs the patterns and a sliding window of texts, and the window slides along the given packed text, matching against stored packed patterns. RESULTS: Three data sets are used to test the performance of the proposed algorithm, and the algorithm was seen to be more efficient than the competitors because its operation is close to machine language. CONCLUSIONS: Theoretical analysis and experimental results both demonstrate that the proposed method outperforms the state-of-the-art methods and is especially effective for the DNA sequence.

Publisher

IOS Press

Subject

Health Informatics,Biomedical Engineering,Information Systems,Biomaterials,Bioengineering,Biophysics

Reference4 articles.

1. Use of the “DNAChecker” algorithm for improving bioinformatics research;Bhat;Makara Journal of Technology,2019

2. EPMA: efficient pattern matching algorithm for DNA sequences;Tahir;Expert Systems with Applications,2017

3. Multi pattern matching algorithm with wildcards based on bit-parallelism;Saif;Wuhan University Journal of Natural Sciences,2017

4. Ordered proposition fusion based on consistency and uncertainty measurements;Liu;Science China Information Sciences,2017

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