한국패류학회지 (The Korean Journal of Malacology)

한국패류학회 (The Malacological Society of Korea)
권호 표지

연체동물 전용 서열 블라스트 서버구축

Construction of BLAST Server for Mollusks

  • 이용석 (한국생명공학연구원 유전체연구센터) ;
  • 조용훈 (순천향대학교 생명과학부) ;
  • 김대수 (한국생명공학연구원 유전체연구센터) ;
  • 김대원 (한국생명공학연구원 유전체연구센터) ;
  • 김민영 (한국생명공학연구원 유전체연구센터) ;
  • 최상행 (한국생명공학연구원 유전체연구센터) ;
  • 연제오 (한국생명공학연구원 유전체연구센터) ;
  • 변인선 (한국생명공학연구원 유전체연구센터) ;
  • 강보라 (한국생명공학연구원 유전체연구센터) ;
  • 정계헌 (순천향대학교 생명과학부) ;
  • 박홍석 (한국생명공학연구원 유전체연구센터)
  • Lee, Yong-Seok (Genome Research Center, Korea Research Institute of Bioscience and Biotechnology) ;
  • Jo, Yong-Hun (Department of Biology, College of Natural Sciences, Soonchunhyang University) ;
  • Kim, Dae-Soo (Genome Research Center, Korea Research Institute of Bioscience and Biotechnology) ;
  • Kim, Dae-Won (Genome Research Center, Korea Research Institute of Bioscience and Biotechnology) ;
  • Kim, Min-Young (Genome Research Center, Korea Research Institute of Bioscience and Biotechnology) ;
  • Choi, Sang-Haeng (Genome Research Center, Korea Research Institute of Bioscience and Biotechnology) ;
  • Yon, Jei-Oh (Genome Research Center, Korea Research Institute of Bioscience and Biotechnology) ;
  • Byun, In-Sun (Genome Research Center, Korea Research Institute of Bioscience and Biotechnology) ;
  • Kang, Bo-Ra (Genome Research Center, Korea Research Institute of Bioscience and Biotechnology) ;
  • Jeong, Kye-Heon (Department of Biology, College of Natural Sciences, Soonchunhyang University) ;
  • Park, Hong-Seog (Genome Research Center, Korea Research Institute of Bioscience and Biotechnology)
  • 발행 : 2004.06.01
PDF 다운로드
⟨ 이전 논문 다음 논문 ⟩

초록

본 연구를 통해서 http://chimp.kribb.re kr/mollusks 에 연체동물 전용 서열 BLAST 데이터베이스가 구축되었다. 예비실험을 통해 본 결과와 마찬가지로 연체동물을 대상으로 한 유전자 정보만을 매우 빠른 속도로 얻을 수 있었다. 본 시스템을 사용하여 앞으로 많은 연구가 진행되어질 연체동물 유전자 연구 및 EST 연구에 많은 도움이 되리라고 사료된다.

The BLAST server for the mollusk was constructed on the basis of the Intel Server Platform SC-5250 dual Xeon 2.8 GHz cpu and Linux operating system. After establishing the operating system, we installed NCBI (National Center for Biotechnology Information) WebBLAST package after web server configuration for cgi (common gate interface) (http://chimp.kribb.re.kr/mollusks). To build up the stand alone blast, we conducted as follows: First, we downloaded the genome information (mitochondria genome information), DNA sequences, amino acid sequences related with mollusk available at NCBI. Second, it was translated into the multifasta format that was stored as database by using the formatdb program provided by NCBI. Finally, the cgi was used for the Stand Alone Blast server. In addition, we have added the vector, Escherichia coli, and repeat sequences into the server to confirm a potential contamination. Finally, primer3 program is also installed for the users to design the primer. The stand alone BLAST gave us several advantages: (1) we can get only the data that agree with the nucleotide sequence directly related with the mollusks when we are searching BLAST; (2) it will be very convenient to confirm contamination when we made the cDNA or genomic library from mollusks; (3) Compared to the current NSBI, we can quickly get the BLAST results on the mollusks sequence information.

키워드