Construction of BLAST server for mollusks = 연체동물 전용 서열 블라스트 서버구축

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Title
Construction of BLAST server for mollusks = 연체동물 전용 서열 블라스트 서버구축
Author(s)
Yong Seok Lee; Y H Jo; Dae Soo Kim; Dae Won Kim; Min Young Kim; Sang-Haeng Choi; Jei Oh Yon; In Sun Byun; Bo Ra Kang; K H Jeong; Hong-Seog Park
Bibliographic Citation
Korean Journal of Malacology, vol. 20, no. 2, pp. 165-169
Publication Year
2004
Abstract
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.
Keyword
BLASTmollusksequenceinformation
ISSN
1225-3480
Publisher
Korea Soc-Assoc-Inst
Type
Article
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1. Journal Articles > Journal Articles
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