Journal
THEORETICAL COMPUTER SCIENCE
Volume 812, Issue -, Pages 137-148Publisher
ELSEVIER
DOI: 10.1016/j.tcs.2019.09.031
Keywords
String matching; Pattern scan order; Scan speed
Categories
Funding
- Institute of Information & Communications Technology Planning & Evaluation (IITP) - Korea government (MSIT) [2018-0-00551]
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In this paper we propose the Maximal Average Shift (MAS) algorithm that finds a pattern scan order that maximizes the average shift length. We also present two extensions of MAS: one improves the scan speed of MAS by using the scan result of the previous window, and the other improves the running time of MAS by using q-grams. These algorithms show better average performances in scan speed than previous string matching algorithms for DNA sequences. (C) 2019 Elsevier B.V. All rights reserved.
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