Journal of Northeastern University Natural Science ›› 2016, Vol. 37 ›› Issue (5): 624-628.DOI: 10.12068/j.issn.1005-3026.2016.05.004

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Multi-core Parallel Substring Matching Algorithm Using BWT

WANG Jia-ying, WANG Bin, LI Xiao-hua, YANG Xiao-chun   

  1. School of Computer Science & Engineering, Northeastern University, Shenyang 110819, China.
  • Received:2015-03-20 Revised:2015-03-20 Online:2016-05-15 Published:2016-05-13
  • Contact: WANG Bin
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Abstract: In order to solve the problem that P-BWT (Burrows-Wheeler transform) could only support short queries, and work on a uniprocessor, a multi-core parallel exact matching algorithm was proposed which any query length could be supposed. Firstly, the search process on P-BWT index was modified. When a query spans multiple data fragments, it first searches on the last segment, then verifies on the other segments. Further, a parallel algorithm was proposed to reduce the iterations in the search and verify process. Finally, the experimental study show that using the proposed algorithm, the substring matching task could be accomplished efficiently in parallel manner.

Key words: BWT(Burrows-Wheeler transform), full text index, exact matching, parallel, multi-core

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