Journal of KIISE:Computer Systems and Theory (한국정보과학회논문지:시스템및이론)

Korean Institute of Information Scientists and Engineers (한국정보과학회)
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Fast Matching Method for DNA Sequences

DNA 서열을 위한 빠른 매칭 기법

  • 김진욱 (인하대학교 컴퓨터정보공학부) ;
  • 김은상 (서울대학교 컴퓨터공학부) ;
  • 안융기 (서울대학교 컴퓨터공학부) ;
  • 박근수 (서울대학교 컴퓨터공학부)
  • Published : 2009.08.15
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Abstract

DNA sequences are the fundamental information for each species and a comparison between DNA sequences of different species is an important task. Since DNA sequences are very long and there exist many species, not only fast matching but also efficient storage is an important factor for DNA sequences. Thus, a fast string matching method suitable for encoded DNA sequences is needed. In this paper, we present a fast string matching method for encoded DNA sequences which does not decode DNA sequences while matching. We use four-characters-to-one-byte encoding and combine a suffix approach and a multi-pattern matching approach. Experimental results show that our method is about 5 times faster than AGREP and the fastest among known algorithms.

DNA 서열은 각 종을 나타내는 근본적인 정보이며, 다른 종 간의 DNA 서열 비교는 중요한 작업이다. DNA 서열은 길이가 매우 길며 또 종의 종류도 다양하기 때문에, DNA 서열 비교에서는 빠른 매칭 뿐만 아니라 효율적인 저장도 중요한 요소이다. 즉, 인코딩 된 DNA 서열에 적합한 빠른 문자열 매칭 방법이 필요하다. 본 논문에서는 매칭 시 디코딩이 필요하지 않은 인코딩 된 DNA 서열을 위한 빠른 매칭 알고리즘을 제시한다. 제시하는 알고리즘은 네 문자 한 바이트 인코딩을 이용하며 서픽스 기법과 다중 패턴 매칭 기법을 접목하고 있다. 실험 결과로는 본 논문에서 제시하는 방법이 AGREP보다 약 다섯배 빠름을 보이는데, 이는 알려진 알고리즘들 중에서 가장 빠른 결과이다.

Keywords

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