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2000 Fiscal Year Final Research Report Summary

Study on the DNA database and other biological databases

Research Project

Project/Area Number 10041187
Research Category

Grant-in-Aid for Scientific Research (A).

Allocation TypeSingle-year Grants
Section海外学術
Research Field 遺伝
Research InstitutionNational Institute of Genetics

Principal Investigator

GOJOBORI Takashi  National Institution of Genetics, Professor Center for Information Biology, 生命情報研究センター, 教授 (50162136)

Co-Investigator(Kenkyū-buntansha) SUGAWARA Hideaki  National Institution of Genetics, Professor Center for Information Biology, 生命情報研究センター, 教授 (80231372)
NISHIKAWA Ken  National Institution of Genetics, Professor Center for Information Biology, 生命情報研究センター, 教授 (10093288)
TATIENO Yoshio  National Institution of Genetics, Professor Center for Information Biology, 生命情報研究センター, 教授 (00202424)
IKEO Kazuho  National Institution of Genetics, Research Associate Center for Information Biology, 生命情報研究センター, 助手 (20249949)
SAITOU Naruya  National Institution of Genetics, Associate Professor Department of Population Genetics, 集団遺伝研究系, 助教授 (30192587)
Project Period (FY) 1998 – 2000
KeywordsDDBJ / EMBL / GenBank / NCBI / INSDB / Human genome / bioinformatics
Research Abstract

Among the results we obtained in our research, "13th International Nucleotide Sequence Database Collaborators Meeting "is most important. we thus mainly report about that. This meeting was held in Bethesda, Maryland, USA, from May l6 to 18, 2000, As the delegate from DDBJ, Professor Yoshio Tateno (Director of DDBJ), Professor Hideaki Sugawara, Dr. Satoshi Miyazaki and three other DDBJ attended it., and they discussed various problems concerning International Nucleotide Sequence Database with the attendants of NCBI (host) and EBB from Europe. The important matters decided at this meeting are as follows. (1) HTG draft sequence quality score assignment. G5 (The five biggest human genome sequencing centers) required assignment of quality score files to GenBank and EMBL.Because similar request was also made to DDBJ from human genome projects in Japan, we decided to correspond with this matter. (2) DDBJ's proposal for creation of new division (FLI) for full length insert cDNA was accepted. (3) DDBJ's proposal for usage of redefined/transl_table= "11" for the case of plastid in gereral, substituting for universal genetic code, /transl_table= "1" was accepted. (4) EMBL proposed clarification of/exception usage, which had been used without clear rules. DDBJ/GenBank agreed with it. (5) GenBank's proposal for use of only one/gene qualifier and addition of/gene_syn as synonyms was rejected by EMBL and DDBJ.Besides, Dr. Takashi Gojobori and other research staffs visited research institutes related to bioinformatics in USA, Australia, Italy, Germany, and China, and investigated construction of databases for bioinformatics and their current usages.

  • Research Products

    (71 results)

All Other

All Publications (71 results)

  • [Publications] Nakamura Y.: "Codon usage tabulated from the international DNA sequence databases"Nucleic Acids Res.. 26. 334 (1998)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] G.Perriere: "The non-redundant Bacillus subtilis (NR Sub) database : update 1998"Nucl.Acids Res.. 26. 60-62 (1998)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Okayama T.: "Formal design and implementation of an improved DDBJ DNA database with a new schema and object-oriented library"Bioinformatics 14, 472-478. 14. 472-478 (1998)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Nakashima H.: "Gene from nine genomes are separated into their organisms in the dinucleotide composition space"DNA Res.5, 251-259. 5. 251-259 (1998)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Tateno Y.: "DNA Data Bank of Japan at work on genome sequence data"Nucleic Acids Research. 26. 16-20 (1998)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Satou K.: "Analysis of HIV by Entropy evolution rate"Amino Acids 14, 343-352. 14. 343-352 (1998)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] OOta S.: "Three Tree : A new method to reconstruct phylogenetic trees"Genome Informatics. 340-341 (1998)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Ren,F.: "Reconstructing molecular phylogenetic tree with multifurcation by using minimum complexity principle"DNA and Molecular Computing. 1825-1828 (1999)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Nakamura,Y.: "Codon usage tabulated from the international DNA sequence databases ; its status 1999"Nucl.Acids Res.. 27・1,. 292 (1999)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Yamazaki,M.: "Genomic organization around the centromeric end of the HLA class I region : Large-scale sequence analysis"J Mol Evol. 48. 317-327 (1999)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Watanabe,M: "A phosphate-induced gene which promotes Penicillium mediated bioconversion ofcis-propenylphosphonic acid to Fosfomycin"Applied and Environmental Microbiology 65,. 65. 1036-1044 (1999)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Nagano N.: "Strong hydrophobic nature of cysteine residues in proteins"FEBS Lett.45,. 45. 69-71 (1999)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Takano K.: "Experimental verification of the "Stability Profile of Mutant Protein" (SPMP) data using mutant human lysozymes"Protein Eng.. 12. 663-672 (1999)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Isogai Y.: "Design and synthesis of a globin fold"Biochemistry. 38. 7431-7443 (1999)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Sugawara H.: "DNA Data Bank of Japan dealing with large-scale data submission"Nucl.Acids.Res.. 27. 25-28 (1999)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Kawabata T.: "The Protein Mutant Database"Nucleic Acids Research. 27・1. 355-357 (1999)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Bellgard,M.: "Significant differences between the G+C content of synonymous codons in orthologous genes and the genomic G+C content"Gene. 238・1. 33-37 (1999)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] OOta S.: "Phylogenetic relationship of muscle tissues deduced from superimposition of gene trees"Mol.Bol.Evol.. 16・6. 856-867 (1999)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Ota M.: "Cooperative approach for the protein fold recognition"Proteins suppl.. 3. 126-132 (1999)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Ota M.: "Feasibility in the inverse protein folding protocol"Protein Sci.. 8. 1001-1009 (1999)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Abola,E.E.: "Quality control in data banks for molecular biology"BioEssays. 22. 1024-1034 (2000)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Tateno,Y.: "DNA Data Bank of Japan in collaboration with mass sequencing teams"Nucleic Acids Res. 28. 24-26 (2000)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Y.Isogai: "Redesign of artificial globins : effects of residue replacements at hydrophobic sites on the structural properties"Biochemistry. 39. 5683-5690 (2000)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Eric S,Lander: "Initial sequencing and analysis of the human genome"Nature. 409・6822. 860-921 (2000)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Suzuki,Y.: "A method for detecting positive selection at single amino acid sites"Mol.Bol.Evol.. 16. 1315-1328 (1999)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Gaudieri,S.: "Different evolutionary histories in two subgenomic regions of the major histocompatibility complex"Genome Research. 9・6. 541-549 (1999)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Bellgard,M.: "Inferring the direction of evolutionary changes of genomic base composition"Trends in Genetics. 15・7. 254-256 (1999)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Itoh,T.: "A low rate of nucleotide changes in Escherichia coli K-12 estimated from a comparison of the genome sequences between two different substrains"FEBS Letters. 450. 72-76 (1999)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Fukami-Kobayashi,K.: "Domain dislocation : a change of core structure in periplasmic binding proteins in their evolutionary history"J.Mol.Biol.. 286. 279-290 (1999)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Yamazaki,M.: "Genomic organization around the centromeric end of the HLA class I region : Large-scale sequence analysis"J Mol Evol. 48. 317-327 (1999)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Okazaki,Y.: "Functional anotation of a full-length mouse cDNA collection"Nature. 409・6821. 685-690 (2001)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Goto,K.: "Genome Information Broker for Data Retrieval and Comparative Analysis of Microbial Genomes"Journal of Japan Society of Information and Knowledge. 10・4. 413 (2001)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] 五條堀孝: "病原性ウイルスはどのように進化したか『遺伝子で生物の進化を考える』"第13回「大学と科学」公開シンポジウム組織委員会. 164 (1999)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] 宮田隆: "総合討論『遺伝子で生物の進化を考える』"第13回「大学と科学」公開シンポジウム組織委員会. 164 (1999)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] 五條堀孝: "科学/技術と人間『地球の生物システム』"岩波講座 第8巻. 241 (1999)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] 五條堀孝: "インターネットを利用したデータベース解析、塩基配列解析『分子生物学プロトコール改訂第2版』"南江堂. 517 (1999)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] 五條堀孝: "情報生物学の時代に向けて-情報の流れとしての生命と進化『続・ロマンチックな科学者』"羊土社. 230 (2000)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] 新井理: "15DNA情報解析『医学・薬学研究者のためのバイオテクノロジー概論』"方編医薬ジャーナル社. 335 (2000)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Nakamura Y.: "Codon usage tabulated from the international DNA sequence databases"Nucleic Acids Res.. 26. 334 (1998)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] G.Perriere: "The non-redundant Bacillus subtilis (NRSub) database : update"Nucl.Acids Res.. 26. 60-62 (1998)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Okayama T.: "Formal design and implementation of an improved DDBJ DNA-database with new schema and object-oriented library"Bioinformatics. 14. 472-478 (1998)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Nakashima H.: "Gene from nine genomes are separated into their organisms in the dinucleotide composition space"DNA Res.. 5. 251-259 (1998)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Tateno Y.: "DNA Data Bank of Japan at work on genome sequence data"Nucleic Acids Research. 26. 16-20 (1998)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Satou K.: "Analysis of HIV by Entropy evolution rate"Amino Acids. 14. 343-352 (1998)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] OOta S.: "Three Tree : A new method to reconstruct phylogenetic trees"Genome Informatics. 1998. 340-341 (1998)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Ren, F.: "Reconstructing molecular phylogenetic tree with multifurcation by using minimum complexity principle"DNA Molecular Computing. 1825-1828 (1999)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Nakamura, Y.: "Codon usage tabulated from the international DNA sequence databases : its status 1999."Nucl.Acids Res.. 27 1. 292 (1999)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Yamazaki, M.: "Genomic organization around the centromeric end of the HLA class I region : Large-scale sequence analysis."J Mol Evol. 48. 317-327 (1999)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Watanabe, M: "A phosphate-induced gene which promotes Penicillium mediated bioconversion ofcis-propenylphosphonic acid to Fosfomycin"Applied and Environmental Microbiology. 65. 1036-1044 (1999)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Nagano N.: "Strong hydrophobic nature of cys-teine residues in proteins"FEBS Lett.. 45. 69-71 (1999)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Takano K.: "Experimental verification of the "Stability Profile of Mutant Protein" (SPMP) data using mutant human lysozymes"Protein Eng.. 12. 663-672 (1999)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Isogai Y.: "Design and synthesis of a globin fold"Biochemistry. 38. 7431-7443 (1999)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Sugawara H.: "DNA Data Bank of Japan dealing with large-scale data submission"Nucl.Acids.Res.. 27. 25-28 (1999)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Kawabata T.: "The Protein Mutant Database"Nucleic Acids Research. 27 1. 355-357 (1999)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Bellgard, M.: "Significant differences between the G+C content of synonymous codons in orthologous genes and the genomic G+C content."Gene. 238 1. 33-37 (1999)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] OOta S.: "Phylogenetic relationship of muscle tissues deduced from suerimposition of gene tress"Mol.Bol.Evol. 16 6. 856-867 (1999)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Suzuki, Y.: "A method for detecting positive selection at single amino acid sites"Mol.Bol.Evol. 16. 1315-1328 (1999)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Gaudieri, S.: "Different evolutionary histories in two subgenomic regions Genome Research of the major histocompatibility complex."Genome Research. 9 6. 541-549 (1999)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Bellgard, M.: "Inferring the direction of evolutionary changes of genomic Trends in Genetics base composition"Trends in Genetics. 15 7. 254-256 (1999)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Itoh, T.: "Alow rate of nucleotide changes in Escherichia cold K-12 estimated from a comparison of the genome sequences between two different substrains"FEBS Letters. 450. 72-76 (1999)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Fukami-Kobayashi, K.: "Domain dislocation : a change of core structure in periplasmic binding proteins in their evolutionary history"J.Mol.Biol.. 286. 279-290 (1999)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Yamazaki, M.: "Genomic organization around the centromeric end of the HLA class I region : Large-scale sequence analysis"J Mol Evol. 48. 317-327 (1999)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Ota M.: "Cooperative approach for the protein fo1d recognition"Protein suppl. 3. 126-132 (1999)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Ota M.: "Feasibility in the inverse protein folding protocol"Protein Sci.. 8. 1001-1009 (1999)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Abola, E.E.: "Quality control in data banks for molecular biology"BioEssays. 22. 1024-1034 (2000)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Tateno, Y.: "DNA Data Bank of Japan in collaboration with mass sequencing teams"Nucleic Acids Res. 28. 24-26 (2000)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Y.Isogai, A.: "Redesign of artificial globins : effects of residue replacrements at hydrophobic sites on the structural properties"Biochemistry. 39. 5683-5690 (2000)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Kikuchi M.: "CAMUS DB : Development of structural database for homology search"Currents in Computational Molecular Biology In Miyano S., Shamir R., and Takagi T.(eds.). 80-81 (2000)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Eric S: "Lander Initial sequepcing and analysis of the human genome"Nature. 409 6822. 860-921 (2001)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Okazaki, Y.: "Functiona1 anotation of full-length mouse cDNA collection"Nature. 409 6821. 685-690 (2001)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Goto, K.: "Genome Information Broker for Data Retrieval and Comparative Analysis of Microbial Genomes."Journal of Japan Society of Information and Knowledge. 10 4. 413 (2001)

    • Description
      「研究成果報告書概要(欧文)」より

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Published: 2002-03-26  

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