国立遺伝学研究所におけるDNAデータバンク:DDBJ
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1 DNA DDBJ Introduction of the DNA Data Bank of Japan (DDBJ) DNA DDBJ DNA Data Bank of Japan 1986 DNA DDBJ GenBankEMBL DDBJDDBJ DDBJ VPP5000 HPCDDBJ DNA DDBJ SE DDBJ Abstract The DNA Data Bank of Japan (DDBJ) was established at the Genetic Code Research Center of the National Institute of Genetics in 1986 to promote DNA sequence registration and research activities. The DDBJ, together with the GenBank of the US and the European EMBL, forms the international base sequence database. The Genetic Code Research Center was established in 1984 and was changed to the Center for Information Biology in Then, in April 2001, the center was changed again to The Center for Information Biology and DNA Data Bank of Japan (CIB/DDBJ). The DDBJ is a public research center and is the main international and public data bank in Japan. Because of its primary position, the DDBJ will play a very important role in the future development of bioinformatics in Japan. The supercomputer system at the National Institute of Genetics is designated as a cooperative facility of Japan. Its HPC system, which includes a VPP5000, is open to external researchers, and the DNA data registration, analysis, and search services of the DDBJ are made available worldwide. Fujitsu has helped the DDBJ to introduce, construct, and operate this supercomputer system and has supplied system engineers to develop and operate the DDBJ services. This paper introduces the DDBJ system and services of the National Institute of Genetics and describes its future development. DDBJ FUJITSU.53, 5, p (09,2002) 353
2 DDBJ/EMBL/GenBank DNA 1, DDBJ DDBJ DDBJ DDBJ DNA Data Bank of Japan EBI/EMBL NCBI/GenBank DNA DDBJ Center for Information Biology and DNA Data Bank of Japan CIB-DDBJ DDBJ CIB-DDBJ CIB DNA CIB-DDBJ DDBJ CIB DDBJ -1 DNA DNA EMBL データライブラリー ( 欧州 ) 設立, 日本へ国際協力 の要請 EMBL,GenBank( 米国 ) が国際協力事業 日本の参加を要請 DNA データバンク運営委員会設置 大学共同利用機関に改組した国立遺伝学研究所に遺 伝情報研究センター設置 遺伝情報研究センターに遺伝情報分析研究室設置 DNA データ研究利用委員会設置 遺伝情報研究センター棟竣工 7 DDBJ リリースの配布開始 9 DDBJ オンライン利用開始 DDBJ リリースに EMBL/GenBank データを加える DDBJ リリースを年 4 回配布へ 遺伝情報研究センターに遺伝子機能研究室新設 遺伝情報研究センターに大量遺伝情報研究室 分子分 類研究室新設 新設の 2 研究室と遺伝情報分析研究室 遺伝子機能研 究室からなる生命情報研究センター設置 生命情報研究センター棟竣工 国立遺伝学研究所にて国際実務者会議 国際諮問委員 会開催 生命情報研究センターの名称が生命情報 DDBJ 研究 センターに改称 -1 DDBJ Fig.1-History of DDBJ, and international cooperation. 354 FUJITSU.53, 5, (09,2002)
3 1983 DDBJ CIB- DDBJ DDBJ DDBJ/EMBL/GenBank DDBJ DNA DDBJ DDBJ Web DDBJ SAKURA DDBJ DDBJ EMBL GenBank DDBJ EMBL GenBank 13 DDBJ/EMBL/GenBank DDBJ/EMBL/GenBank DNA RNA DDBJ/EMBL/GenBank DNA 3 DDBJ/EMBL/GenBank DNA DNA DNA 1, DDBJ -2 DDBJ/EMBL/GenBank Fig.2-DDBJ/EMBL/GenBank International Nucleotide Sequence Database. ( 万件 ) 2,000 1,800 1,600 1,400 1,200 1, エントリ数 年 1.5~2.0 倍の伸び ( 西暦 ) -3 Fig.3-International Nucleotide Sequence Database Growth. FUJITSU.53, 5, (09,2002) 355
4 DNA DBJ/EMBL/GenBank DDBJ 15-4 DDBJ DDBJ DNA DDBJ top -5 DDBJ 1 DNA- SAKURA 2 FASTA BLAST SSEARCH 10 SRS Sequence Retrieval System DDBJ XML DDBJ-XML 3 VPP5000 PRIMEPOWER2000 DDBJ -6 4 GIB Genome Information Broker -7 5 DB PDB DDBJ Homo sapiens ( ヒト ) Mus musculus ( マウス ) Rattus norvegicus ( ラット ) Drosophila melanogaster ( キイロショウジョウバエ ) Arabidopsis thaliana ( シロイロナズナ ) Oryza sativa (japonica cultivar-group) ( イネ ) Caenorhabditis elegans ( エレバンス線虫 ) Oryza sativa ( イネ ) Brassica oleracea ( キャベツ ) Tetraodon nigroviridis ( ミドリフグ ) Pan troglodytes ( チンパンジー ) Danio rerio ( ゼブラフィッシュ ) Zea mays ( トウモロコシ ) Bos taurus ( ウシ ) Glycine max ( ダイズ ) Fig.4-Top 15 organisms according to the total number of nucleotides. -5 DDBJTop (4) Fig.5-Top page of DDBJ website. 356 FUJITSU.53, 5, (09,2002)
5 -6 DDBJ Fig.6-Supercomputer systems of DDBJ. -8 XML Central of DDBJ Fig.8-System image of XML Central of DDBJ. -7 GIB Fig.7-A sample of GIB (Genome Information Broker) services. DDBJ Web DDBJ DDBJ XML Web XML Central of DDBJ XML Central of DDBJ -8 1 Getentry DDBJ PIR SwissProt PDB PRF ProteinID 2 BLAST BLAST 3 FASTA FASTA 4 CLUSTALW CLUSTALW 5 SRS 20 DB 6 TxSearch Taxonomy Database 7 DDBJ DDBJ Feature 8 DDBJ Web DDBJ DDBJ DDBJ FUJITSU.53, 5, (09,2002) 357
6 DDBJ DDBJ 3 3 DDBJ DDBJ 2 DDBJ 1 DDBJ DDBJ DNA 2 DDBJ DDBJ/CIB 3 DDBJ DDBJ 4 DDBJ URL FUJITSU.53, 5, (09,2002)
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