Korean Journal of Microbiology (미생물학회지)

The Microbiological Society of Korea (한국미생물학회)
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NOGSEC: A NOnparametric method for Genome SEquence Clustering

녹섹(NOGSEC): A NOnparametric method for Genome SEquence Clustering

  • 이영복 (부산대학교 전자계산학과 그래픽스응용연구실, 포항공과대학교 생물학전문연구정보센터) ;
  • 김판규 (부산대학교 전자계산학과 그래픽스응용연구실, 컴퓨터 및 정보통신연구소) ;
  • 조환규 (부산대학교 전자계산학과 그래픽스응용연구실, 컴퓨터 및 정보통신연구소)
  • Published : 2003.06.01
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Abstract

One large topic in comparative genomics is to predict functional annotation by classifying protein sequences. Computational approaches for function prediction include protein structure prediction, sequence alignment and domain prediction or binding site prediction. This paper is on another computational approach searching for sets of homologous sequences from sequence similarity graph. Methods based on similarity graph do not need previous knowledges about sequences, but largely depend on the researcher's subjective threshold settings. In this paper, we propose a genome sequence clustering method of iterative testing and graph decomposition, and a simple method to calculate a strict threshold having biochemical meaning. Proposed method was applied to known bacterial genome sequences and the result was shown with the BAG algorithm's. Result clusters are lacking some completeness, but the confidence level is very high and the method does not need user-defined thresholds.

비교유전체학의 주요 주제 중 유전자서열을 분류하고 단백질기능을 예측하는 연구가 있으며, 이를 위해 단백질 구조, 공통서열 및 바인딩 위치 예측등의 방법과 함께, 전유전체 서열에서 구해지는 유사도 그래프를 분석해 상동유전자를 검색하는 계산학적인 접근방법이 있다. 유사도그래프를 사용한 방법은 서열에 대한 기존 지식에 의존하지 않는 장점이 있지만 유사도 하한값과 같은 주관적인 임계값이 필요한 단점이 있다. 본 논문에서는 반복적으로 그래프를 분해하는 이전의 방법을 일반화시켜, 유사도 그래프에 기반한 유전자 서열군집분석 방법론과 객관적이고 안정적인 파라미터 임계값 계산 방법을 제안한다. 제시된 방법으로 알려진 미생물 유전체 서 열을 분석하여 이전의 방법인 BAG 알고리즘 결과와 비교했다.

Keywords

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