KSBB Journal

The Korean Society for Biotechnology and Bioengineering (한국생물공학회)
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Prediction of ORFs in Metagenome by Using Cis-acting Transcriptional and Translational Factors

메타게놈 서열에 존재하는 보존적인 전사와 번역 인자를 이용한 ORF 예측

  • Cheong, Dea-Eun (Department of Biological Sciences, College of Natural Sciences, Chonnam National University) ;
  • Kim, Geun-Joong (Department of Biological Sciences, College of Natural Sciences, Chonnam National University)
  • Received : 2010.09.10
  • Accepted : 2010.10.24
  • Published : 2010.10.31
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Abstract

As sequencing technologies are steadily improving, massive sequence data have been accumulated in public databases. Thereby, programs based on various algorithms are developed to mine useful information, such as genes, operons and regulatory factors,from these sequences. However, despite its usefulness in a wide range of applications, comprehensive analyses of metagenome using these programs have some drawbacks, thereby yielding inaccurate or complex results. We here provide a possibility of signature sequences (cis-acting transcriptional and translational factors of metagenome) as a hallmark of ORFs finding from metagenome.

미생물은 지구상에 약 $5\;{\times}\;10^{30}$ 정도의 개체가 존재하며, 350~550 Pg (1Pg = 1015g)의 탄소, 85~130 Pg의 질소, 9~14 Pg의 인 등, 지구상의 어떠한 생물 종보다 거대한 양의 원소를 포함하고 있다. 또한 이러한 미생물과 생태계를 구성하는 다른 유기체나 무기물과의 관계가 지속적으로 밝혀지고 있다. 이러한 연구들의 기본적인 목표는 상호작용에 중요한 인자들의 규명 (대표적으로 유전자)하는 것이기 때문에, 염색체에 존재하는 true ORF의 검색과 확인은 가장 중요한 기본 수단이 된다. 그러나 다양한 미생물로 구성된 환경 유전체는 기존 정보로 검색 가능한 비율을 정확하게 유추할 수 없기에 많은 어려움이 있다. 이렇게 경계가 불분명한 자료의 검색을 위해서는 보다 많은 정보를 필요 (training이나 space를 규정하기 위한 보다 많은 유전자 서열)로 하며, 다른 검색 방법이나 기법들이 추가적으로 개발되어야 할 것이다. 이러한 방법의 대안으로써, 미생물의 유전자간 서열에 존재하는 전사/번역인자의 보존성에 근거한 검색방법은 개량 여하에 따라 광범위한 적용 범위를 지닐 것이다. 현 수준에서도 조합 탐색, 즉 기존의 방법과 혼용하거나 기존의 방법을 보완하는 과정으로 충분한 가치를 지니고 있다. 이러한 추정은, 기존의 ORF 중심의 발굴 결과와 전혀 일치되지 않는 경우에서부터 90% 이상 일치하는 등의 결과로서 확인하였다. 일치 되지 않는 많은 경우가 BLASTing으로 검색되지 않는 새로운 ORF를 포함하기 때문이다.

Keywords

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