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

Korean Institute of Information Scientists and Engineers (한국정보과학회)
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Linear-Time Search in Suffix Arrays

접미사 배열을 이용한 선형시간 탐색

  • Published : 2005.06.01
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Abstract

To search a pattern P in a text, such index data structures as suffix trees and suffix arrays are widely used in diverse applications of string processing and computational biology. It is well known that searching in suffix trees is faster than suffix ways in the aspect of time complexity, i.e., it takes O(${\mid}P{\mid}$) time to search P on a constant-size alphabet in a suffix tree while it takes O(${\mid}P{\mid}+logn$) time in a suffix way where n is the length of the text. In this paper we present a linear-tim8 search algorithm in suffix arrays for constant-size alphabets. For a gene.al alphabet $\Sigma$, it takes O(${\mid}P{\mid}log{\mid}{\Sigma}{\mid}$) time.

계산 생물학이나 문자열 연구 분야에 다양하게 웅용되는 패턴 탐색 문제에 접미사 트리와 접미사 배열과 같은 인덱스 자료구조가 널리 사용되어 왔다. 접미사 트리를 이용한 패턴 탐색이 접미사 배열을 이용한 탐색보다 시간 복잡도 관점에서 더 빠른 것으로 알려져 왔다. 즉, 상수 크기의 알파벳에 대해 패턴 P를 길이 n인 텍스트에서 탐색하기 위해 접미사 트리는 O(${\mid}P{\mid}$)시간이 필요한 반면 접미사 배열은 O(${\mid}P{\mid}+ logn$) 시간이 필요하다. 본 논문에서는 상수 크기 알파벳에 대해 접미사 배열을 이용한 선형시간 탐색 알고리즘을 제시한다. 본 알고리즘은 일반적인 알파벳 $\Sigma$에 대해서는 O(${\mid}P{\mid}log{\mid}{\Sigma$)시간이 필요하다.

Keywords

References

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