The Korean Journal of Malacology (한국패류학회지)

The Malacological Society of Korea (한국패류학회)
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Mollusks Sequence Database: Version II

연체동물 전용 BLAST 서버 업데이트 (Version II)

  • Kang, Se Won (Department of Life Science, Soonchunhyang University) ;
  • Hwang, Hee Ju (Department of Life Science, Soonchunhyang University) ;
  • Park, So Young (Department of Life Science, Soonchunhyang University) ;
  • Wang, Tae Hun (Department of Life Science, Soonchunhyang University) ;
  • Park, Eun Bi (Department of Life Science, Soonchunhyang University) ;
  • Lee, Tae Hee (Department of Architecture, Soonchunhyang University) ;
  • Hwang, Ui Wook (Department of Biology Education, Teacher's College, Kyoungpook National University) ;
  • Lee, Jun-Sang (Institute of Environmental Research, Kangwon National University) ;
  • Park, Hong Seog (Research Institute of GnC BIO Co., LTD.) ;
  • Han, Yeon Soo (Division of Plant Biotechnology, College of Agriculture and Life Sciences, Chonnam National University) ;
  • Lim, Chae Eun (Biological and Genetic Resources Assessment Division, National Institute of Biological Resources) ;
  • Kim, Soonok (Biological and Genetic Resources Assessment Division, National Institute of Biological Resources) ;
  • Lee, Yong Seok (Department of Life Science, Soonchunhyang University)
  • 강세원 (순천향대학교 자연과학대학 생명시스템학과) ;
  • 황희주 (순천향대학교 자연과학대학 생명시스템학과) ;
  • 박소영 (순천향대학교 자연과학대학 생명시스템학과) ;
  • 왕태훈 (순천향대학교 자연과학대학 생명시스템학과) ;
  • 박은비 (순천향대학교 자연과학대학 생명시스템학과) ;
  • 이태희 (순천향대학교 공과대학 건축학과) ;
  • 황의욱 (경북대학교 사범대학 생물교육학과) ;
  • 이준상 (강원대학교 환경연구소) ;
  • 박홍석 ((주)지앤시바이오) ;
  • 한연수 (전남대학교 농업생명과학대학 식물생명공학부) ;
  • 임채은 (국립생물자원관 유용자원분석과) ;
  • 김순옥 (국립생물자원관 유용자원분석과) ;
  • 이용석 (순천향대학교 자연과학대학 생명시스템학과)
  • Received : 2014.12.20
  • Accepted : 2014.12.27
  • Published : 2014.12.31
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Abstract

Since we reported a BLAST server for the mollusk in 2004, no work has reported the usability or modification of the server. To improve its usability, the BLAST server for the mollusk has been updated as version II (http://www.malacol.or.kr/blast) in the present study. The database was constructed by using the Intel server Platform ZSS130 dual Xeon 3.20 GHz CPU and Linux CentOS system and with NCBI WebBLAST package. We downloaded the mollusk nucleotide, amino acid, EST, GSS and mitochondrial genome sequences which can be opened through NCBI web BLAST and used them to build up the database. The updated database consists of 520,977 nucleotide sequences, 229,857 amino acid sequences, 586,498 EST sequences, 23,112 GSS and 565 mitochondrial genome sequences. Total database size is 1.2 GB. Furthermore, we have added repeat sequences, Escherichia coli sequences and vector sequences to facilitate data validation. The newly updated BLAST server for the mollusk will be useful for many malacological researchers as it will save time to identify and study various molluscan genes.

본 연구를 통하여 연체동물 전용 BLAST 서버 (Version II)가 웹주소 http://www.malacol.or.kr/blast에 구축되었다. 연체동물을 대상으로 하는 연구에 있어 필요한 정보를 매우 빠르게 얻을 수 있었다. 본 시스템을 사용하여 앞으로도 많은 연구가 진행되어지길 바라며, 아울러 많은 연체동물 연구자들에게 많은 도움이 되리라고 사료된다.

Keywords

References

  1. Altschul, S. F., Gish, W., Miller, W., Myers, E. W. and Lipman, D. J. (1990) Basic local alignment search tool. Journal of molecular biology, 215: 403-410. https://doi.org/10.1016/S0022-2836(05)80360-2
  2. McGinnis, S. and Madden, T. L. (2004) BLAST: at the core of a powerful and diverse set of sequence analysis tools. Nucleic acids research, 32: W20-W25 https://doi.org/10.1093/nar/gkh435
  3. Lee, Y. S., Jo, Y. H., Kim, D. S., Kim, D. W., Kim, M. Y., Choi, S. H., Yon, J. O., Byun, I. S., Kang, B. R., Jeong, K. H. and Park, H. S. (2004) Construction of BLAST Server for Mollusks. Korean journal of malacology, 20:165-169.

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