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Pattern Matching with Flexible Wildcard Gaps

  • Zhang Junyan
  • Yang Chenhui
Conference paper
Part of the Lecture Notes in Electrical Engineering book series (LNEE, volume 269)

Abstract

Pattern matching is a fundamental application in biomedicine and biological sequence analysis. A wildcard can match any one character in a sequence. Multiple wildcards form a gap. A flexible wildcard gap can match any characters with specific length which is specified by users. Therefore, the effective algorithm performing this kind of matching is in great need. In this paper, we design PMFG algorithm and achieve it by dividing a pattern into multiple subpatterns with different length based on gap segmentation. After computing the starting positions and ending positions of each subpattern, the effective intervals and effective starting positions can be determined one by one. The number of the elements in the last effective position set equals to the number of the matching. A comparison experiments are done based on three DNA sequences. The results show that PMFG algorithm has better performance in the same fields.

Keywords

Pattern matching Wildcard gap Sequence 

References

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Copyright information

© Springer Science+Business Media Dordrecht 2014

Authors and Affiliations

  1. 1.Information Science and Technology CollegeChengdu UniversityChengduChina
  2. 2.Key Laboratory of Pattern Recognition and Intelligent Information Processing of SichuanChengdu UniversityChengduChina

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