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Prediction of gene functions by use of molecular evolutionary approach

Research Project

Project/Area Number 07504009
Research Category

Grant-in-Aid for Scientific Research (A)

Allocation TypeSingle-year Grants
Section展開研究
Research Field 遺伝
Research InstitutionNational Institute of Genetics

Principal Investigator

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

Co-Investigator(Kenkyū-buntansha) IMANISHI Tadashi  National Institute of Genetics, Center for Information Biology Assistant Profess, 生命情報研究センター, 助手 (80270461)
IKEO Kazuho  National Institute of Genetics, Center for Information Biology Assistant Profess, 生命情報研究センター, 助手 (20249949)
TATENO Yoshio  National Institute of Genetics, Center for Information Biology, Professor, 生命情報研究センター, 教授 (00202424)
IKEMURA Toshimichi  National Institute of Genetics, Department of Population Genetics, Professor, 集団遺伝研究系, 教授 (50025475)
MIYATA Takashi  Kyoto University, Dept.of Biophysics, Professor, 理学部, 教授 (20022692)
内藤 公敏  富士通第6システム統括部, 第4システム課, 課長
Project Period (FY) 1995 – 1997
Project Status Completed (Fiscal Year 1997)
Budget Amount *help
¥20,500,000 (Direct Cost: ¥20,500,000)
Fiscal Year 1997: ¥9,500,000 (Direct Cost: ¥9,500,000)
Fiscal Year 1996: ¥11,000,000 (Direct Cost: ¥11,000,000)
Keywordsmolecular evolution / prediction of gene function / functional domain / Molecular Phylogenetic Tree / serine protease / MHC (major histocompatibility complex) / nucleotide sequence / sequencing / セリンプロテアーゼ
Research Abstract

The main purpose of the present research project is to extract functional domains from the nucleotide sequences of homologous gene groups by use of molecular evolutionary approach. To attain this purpose, we first developed the the new method for constructing phylogenetic trees based upon the minimum description length principle. By using this new method, we identified several functional domains of serine protease genes as an example. Because this method was so successful, weextended our approach to all homologous gene groups. Then, we constructed the 'so-called' sequence motif database, where sequence motif represents characteristics of the sequence specific to a particular function. Moreover, we produced nucleotide sequences of genes whose data availability is sos limited by conducting the PCR experiments. In order to establish the sequence techniques in our laboratory, we practiced the PCR experiment by using fish mitochondrial DNAs. These results obtained in this research project is significant for identifying and predicting the gene functions from the nucleotide sepuence data.

Report

(4 results)
  • 1997 Annual Research Report   Final Research Report Summary
  • 1996 Annual Research Report
  • 1995 Annual Research Report
  • Research Products

    (69 results)

All Other

All Publications (69 results)

  • [Publications] Endo, T.: "Evolutionary significance of intra-genome duplications on human chromosomes" GENE. 205. 9-27 (1997)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1997 Final Research Report Summary
  • [Publications] Watanabe, H.: "Bacteril features in the genome of methanococcus jannaschii in terms of gene composition and biased base composition in ORFs and their Surrounding regions." GENE. 205. 7-18 (1997)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1997 Final Research Report Summary
  • [Publications] Okamoto, Y.: "Father-to-mother-to-infant transmission of HTV-1:clonally transmitted isolate of infant mutates more rapidly than that of the mother and rapidly loses reactivity with neutralizing antibody" Microbiol Immunol. 41. 131-138 (1997)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1997 Final Research Report Summary
  • [Publications] Kurihara, T.: "Molecular evolution of myelin proteolipid protein." Biochemical and Biophysical Research Communications. 237. 559-561 (1997)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1997 Final Research Report Summary
  • [Publications] Tanaka, H.: "Inference of molecular phylogenetic tree based on minimum model-based complexity method." Proceedings of Fifth internationa1 conference on intelligent systems for molecular biology.319-328 (1997)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1997 Final Research Report Summary
  • [Publications] Sato, S.: "Ascidiln tyrosinase gene:Its unique structure and expression in the developing brain." Developmental Dynamics. 208. 363-374 (1997)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1997 Final Research Report Summary
  • [Publications] Watanabe, H.: "Genome plasticity as a paradigm of eubacteria evolution." J.Mol.Evo1.44. 57-64 (1997)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1997 Final Research Report Summary
  • [Publications] Tateno, Y: "Evolutionary motif and its biological and structural significance." J.Mo1.Evol.44. 38-43 (1997)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1997 Final Research Report Summary
  • [Publications] Taniguchi.Y: "Gloning,sequencing,and chromosomal localization of two tandemly arranged human pseudogenes for the proliferating cell nuclear antigen" Mammalian Genome. 7. 906-908 (1996)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1997 Final Research Report Summary
  • [Publications] Endo, T.: "Large-scale search for genes on which positive selection may operate." Mo1.Biol.Evo1.13. 685-690 (1995)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1997 Final Research Report Summary
  • [Publications] Gojobori, T.: "Domain evolution of serine protease and its inhibitor genes.In:Tracing Biological Evolution in Protein and Gene Structures.(Eds,M Go and P.Schimmel)" Proceedings of the 20th Taniguchi International Symposium,Divstion of Biophysics. Elsevier Science B.V.249-260 (1995)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1997 Final Research Report Summary
  • [Publications] Gojobori, T.: "Evolution of genes and the DNA database-Implications for bioremediation-In:Bioremediation:the Tokyo'94 workshop." OECD Documents. 369-373 (1995)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1997 Final Research Report Summary
  • [Publications] Gojobori.T.: "Genetic diversity and molecular evolution of pathogenic viruses." Biology International. 33. 30 (1995)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1997 Final Research Report Summary
  • [Publications] Shiina, T.: "Isolation and characterization of cDNA clones for Japanese quail(Coturnix japonica)major histocompatibility complex(MhcCoja)class Imolecules." Immunogenetics. 42. 213-216 (1995)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1997 Final Research Report Summary
  • [Publications] Gojobori, T.: "Sequence divergence estimation.In:Molecular Biology and Biotechnology.A Comprehensive Desk Reference.(Ed.,R.A.Meyers)" VCH Publishers,Inc.863-866 (1995)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1997 Final Research Report Summary
  • [Publications] Ikeo, K.: "Different evolutionary histories of kringle and protease domains in serine proreases-A typical example of domain evolution." J.Mol.Evo1.40. 331-336 (1995)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1997 Final Research Report Summary
  • [Publications] 山口 由美: "ウイルスの分子進化" ウイルス. 第46巻. 1-6 (1996)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1997 Final Research Report Summary
  • [Publications] 五條掘 孝: "ゲノムから生物を考える" 分子生物学の新たな地平をめざして. Vol.15. 485-490 (1996)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1997 Final Research Report Summary
  • [Publications] 今西 規: "『ネオ生物学シリーズ(9)ヒト』榊 佳之、村松正實編集" 共立出版, 154 (1997)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1997 Final Research Report Summary
  • [Publications] 五條掘 孝: "『エボルーション』" 共立出版, 2767 (1997)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1997 Final Research Report Summary
  • [Publications] Endo T.et al.: ""Evolutionary significance of intra-genome duplications on human chromosomes."" GENE. 205. 9-27 (1997)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1997 Final Research Report Summary
  • [Publications] Watanabe H.et al.: ""Bacterial features in the genome of methanococcus jannaschii in terms of gene composition and biased base composition in ORFs and their surrounding regions."" GENE. 205. 7-18 (1997)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1997 Final Research Report Summary
  • [Publications] Okamoto Y.et al.: ""Father-to-mother-to-in fant transmission of HIV-1 : clonally transmitted isolate of ingant mutates more rapidly than that of the mother and rapidly loses reactivity with neutralizing antibody."" Microbilo Immunol. 41 : (2). 131-138 (1997)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1997 Final Research Report Summary
  • [Publications] Kurihara, T.et al.: ""Molecular evolution of myelin proteolipid protein"." Biochemical and Biophysical Research Communications.237. 559-561 (1997)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1997 Final Research Report Summary
  • [Publications] Tanaka, H.et al.: ""Inference of moleculara phylogenetic tree based on minimum model-based complexity method."" Proceedings of Fifth international conference on intelligent systems for molecular biology. 319-328 (1997)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1997 Final Research Report Summary
  • [Publications] Sato, S.et al.: ""Ascidian tyrosinase gene : Its unique structure and expression in the developing brain."" Developmental Dynamics. 208. 363-374 (1997)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1997 Final Research Report Summary
  • [Publications] Watanabe H.et al.: ""Genome plasticity as a paradigm of eubacteria evolution."" J.Mol.Evol. 44. 57-64 (1997)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1997 Final Research Report Summary
  • [Publications] Tateno, Y.et al.: ""Evolutionary motif and its biological and structural significance."" J.Mol.Evol. 44. 38-43 (1997)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1997 Final Research Report Summary
  • [Publications] Taniguchi, Y.et al.: ""Cloning, sequencing, and chromosomal localization of two tandemly arranged human pseudogenes for the proliferating cell nuclear antigen (PCNA)."" Mammalian Genome. 7. 906-908 (1996)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1997 Final Research Report Summary
  • [Publications] Endo, T.et al.: ""Large-scale seach for genes on which positive selection may operate."" Mol.Biol.Evol.13. 685-690 (1996)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1997 Final Research Report Summary
  • [Publications] Gojobori, T.et al.: ""Domain evolution of serine protease and its inhibitor genes. In : Tracing Biological Evolution in Protein and Gene Structures."" Proceedings of the 20th Taniguchi International Symposium, Div. of Biophysics.249-260 (1995)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1997 Final Research Report Summary
  • [Publications] Gojobori, T.et al.: ""Evolution of genes and the DNA database-Implications for bioremediation-."" Bioremediation : the Tokyo'94 Workshop. OECD Documents. Symposium, Div. of Biophysics.369-373 (1995)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1997 Final Research Report Summary
  • [Publications] Gojobori, T.et al.: ""Genetic diversity and molecular evolution of pathogenic viruses."" Biology International. 33. 30 (1995)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1997 Final Research Report Summary
  • [Publications] Shiina, T.et al.: ""Isolation and characterization of cDNA clones for Japanese quail (Coturnix japonica) major histocompatibility complex (MhcCoja) class I molecules."" Immunogenetics. 42. 213-216 (1995)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1997 Final Research Report Summary
  • [Publications] Gojobori, T.et al.: ""Sequence divergence estimation. In : Molecular Biology and. Biotechnology. A Comprehensive Desk Reference."" VCH Publichers, Inc.863-866 (1995)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1997 Final Research Report Summary
  • [Publications] Ikeo, K.et al.: ""Different evolutionary histories of kringle and protease domains in serine proteases-A typical example of domain evolution."" J.Mol.Evol.40. 331-336 (1995)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1997 Final Research Report Summary
  • [Publications] Tateno Y.: "Evolutionary motif and its biological and structural significance." J.Mol.Evol.44・1. 38-43 (1997)

    • Related Report
      1997 Annual Research Report
  • [Publications] Watanabe H.: "Genome plasticity as a paradigm of eubacteria evolution." J.Mol.Evol.44・1. 57-64 (1997)

    • Related Report
      1997 Annual Research Report
  • [Publications] Kurihara T.: "Molecular evolution of myelin proteolipid protein." Biochemical and Biophysical Research Communications.237. 559-561 (1997)

    • Related Report
      1997 Annual Research Report
  • [Publications] Watanabe H.: "Bacterial features in the genome of methanococcus jannaschii in terms of gene composition and biased base composition in ORFs and their surrounding regions." GENE. 205. 7-18 (1997)

    • Related Report
      1997 Annual Research Report
  • [Publications] Endo T.: "Evolutionary significance of intra-genome duplications on human chromosomes" GENE. 205. 9-27 (1997)

    • Related Report
      1997 Annual Research Report
  • [Publications] Sato S.: "Ascidian tyrosinase gene:Its unique structure and expression in the developing brain." Developmental Dynamics. 208. 363-374 (1997)

    • Related Report
      1997 Annual Research Report
  • [Publications] Suzuki Y.: "The origin and evolution of human T-Cell lymphotrophic virus type I and II" Virus Genes. 16・1. 69-84 (1998)

    • Related Report
      1997 Annual Research Report
  • [Publications] Perrie reG.: "The NRSub database:update 1997." Nucl.Acids Res.25・1. 53-56 (1997)

    • Related Report
      1997 Annual Research Report
  • [Publications] Nakamura Y.: "Codon usage tabulated from the international DNA sequence databases." Nucl.Acids Res.25・1. 244-245 (1997)

    • Related Report
      1997 Annual Research Report
  • [Publications] Mizokami M.: "Constrained evolution of hepatitis B virus with overlapping genes." J.Mol.Evol.44・1. 83-90 (1997)

    • Related Report
      1997 Annual Research Report
  • [Publications] Yamaguchi Y.: "Evolutionary mechanisms and population dynamics of the third variable envelope region of HIV within single hosts." Proc.Natl.Acad.Sci.U.S.A. 94. 1264-1269 (1997)

    • Related Report
      1997 Annual Research Report
  • [Publications] Tenzen T.: "Precise switching of DNA replication timing in the GC content transition area in the human Major Histocompatibility Complex." Mol.and Celular Biology. 17・7. 4043-4050 (1997)

    • Related Report
      1997 Annual Research Report
  • [Publications] Suzuki Y.: "The origin and evolution of ebola and marburg viruses." Mol.Biol.Evol.14・8. 800-806 (1997)

    • Related Report
      1997 Annual Research Report
  • [Publications] Kurihara T.: "Molecular evolution of myelin proteolipid protein." Biochemical and Biophysical Research Communications.237. 559-561 (1997)

    • Related Report
      1997 Annual Research Report
  • [Publications] Mizuki N.: "Major histocompatibility complex class II allelles in Kazak and Han populations in the Silk Route of northwestern China." Tissue Antigens. 50. 527-534 (1997)

    • Related Report
      1997 Annual Research Report
  • [Publications] Okamoto Y.: "Father-to-mother-to-infant transmission of HIV-1:clonally transmitted isolate of infant mutates more rapidly than that of the mother and rapidly loses reactivity with neutralizing antibody." Microbiol Immunol. 41・2. 131-138 (1997)

    • Related Report
      1997 Annual Research Report
  • [Publications] Perriere,G.: "NRSub : a non-redundant database for Bacillus subtilis." Nucl.Acids Res.24・1. 41-45 (1996)

    • Related Report
      1996 Annual Research Report
  • [Publications] Ohba,K.: "Evolutionary relationship of hepatitis C,pesti-,flavi-,plantviruses,and newly discovered GB hepatitis agents." FEBS Lett.378. 232-234 (1996)

    • Related Report
      1996 Annual Research Report
  • [Publications] Endo,T.: "Large-scale search for genes on which positive selection may operate." Mol.Biol.Evol.13・5. 685-690 (1996)

    • Related Report
      1996 Annual Research Report
  • [Publications] Fumihito A.: "Monophyletic origin and unique dispersal Patterns of domestic fowls." Proc.Natl.Acad.Sci.93・13. 6792-6795 (1996)

    • Related Report
      1996 Annual Research Report
  • [Publications] Shiga,H.: "Identification of multiple HIV-1 cytotoxic T-cell epitopes presented by human leukocyte antigen B35molecules." AIDS. 10. 1075-1083 (1996)

    • Related Report
      1996 Annual Research Report
  • [Publications] Gojobori,T.: "DNA database and its applications to the study of molecular evolution." Bio Japan′96.355-359 (1996)

    • Related Report
      1996 Annual Research Report
  • [Publications] Imanishi,T.: "Diversity in human MHC genes among ethnic groups worldwide. In ; Etnnoepidemiology of Cancer." Gann Monograph on Cancer Research. 44. 89-96 (1996)

    • Related Report
      1996 Annual Research Report
  • [Publications] Koike,T.: "Development of new DDBJ DNA sequence database with data annotation tool Yamato II." Proceeding of the seventh workshop on Genome Informatics 1996. 7. 157-165 (1996)

    • Related Report
      1996 Annual Research Report
  • [Publications] Taniguchi,Y.: "Large-scale search for genes on which positive selection may operate." Mammalian Genome. 7. 906-908 (1996)

    • Related Report
      1996 Annual Research Report
  • [Publications] Kitakami,H.: "YAMATO AND ASUKA:DNA Database Management System." Proceedings of the 28th Annual Hawaii Int'l Conf.on System Sciences.5. 72-80 (1995)

    • Related Report
      1995 Annual Research Report
  • [Publications] Ren,F: "Molecular Evolutionary Phylogenetic Trees Based on Minimum Description Length Principle." Proceedings of the 28th Annual Hawaii Int'l Conf.on System Sciences.5. 165-173 (1995)

    • Related Report
      1995 Annual Research Report
  • [Publications] Ren,F: "Construction of Molecular Evolutionary Phylogenetic Trees from DNA Sequences Based on Minimum Complexity Principle." Computer methods and programs in Biomedicine,Elsevier. 46. 121-130 (1995)

    • Related Report
      1995 Annual Research Report
  • [Publications] Ikeo,K.: "Different Evolutionary Histories of Kringle and Protease Domains in Serine Proteases-A Typical Example of Domain Evolution." Journal of Mol.Evol.40. 331-336 (1995)

    • Related Report
      1995 Annual Research Report
  • [Publications] Shiina,T.: "Isolation and characterization of cDNA clones for Japanese quail(Coturnixjaponica)major histocompatibility complex(MhcCoja)class I molecules." Immunogenetics. 42. 212-216 (1995)

    • Related Report
      1995 Annual Research Report
  • [Publications] Geng,L.: "Determination of HLA class II alleles by genotyping in a Manchu population in the northern part of China and its relationship with Han and Japanese populations." Tissue Antigens. 46. 111-116 (1995)

    • Related Report
      1995 Annual Research Report
  • [Publications] Gojobori,T.: "Molecular Biology and Biotechnology.:A Comprehensive Desk Reference.(Ed.R.A.Meyers)" VCH Publishers,Inc., 1034 (1995)

    • Related Report
      1995 Annual Research Report
  • [Publications] Gojobori,T.: "Tracing Biological Evolution in Protein and Gene Structures.(Eds.M.Go and P.Schimmel)" Elsevier Science B.V., 314 (1995)

    • Related Report
      1995 Annual Research Report

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Published: 1996-04-01   Modified: 2016-04-21  

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