Journal of Northeastern University Natural Science ›› 2019, Vol. 40 ›› Issue (11): 1543-1548.DOI: 10.12068/j.issn.1005-3026.2019.11.005

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A Novel Similarity Verification Algorithm Under Edit Distance Limitation

YU Chang-yong, LI Miao-miao, ZHAO Chu, MA Hai-tao   

  1. School of Computer & Communication Engineering, Northeastern University at Qinhuangdao, Qinhuangdao 066004, China.
  • Received:2019-03-13 Revised:2019-03-13 Online:2019-11-15 Published:2019-11-05
  • Contact: LI Miao-miao
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Abstract: For the high complexity problem of edit distance calculation in the similarity confirmation step, a string similarity confirmation algorithm based on pigonhole principle under the limitation of edit distance is proposed. Firstly, it found a segment satisfies the edit distance segment mapping, then based on this segment, the read length of 500bp was segmented. Then the edit distance of right and left parts was calculated and all parts sum to the final result. Finally, based on the longest common substring, the number of segments to be verified is minimized, and an optimization scheme was obtained. The experimental result show that this verification algorithm reduces the time of the verification step, and ensures the zero false positive and false negative rate.

Key words: read mapping, edit distance, similarity search, pigonhole principle, verification algorithm

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