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1995 Fiscal Year Final Research Report Summary

"Development of a method for accurate determination of nucleotide sequences using a DNA sequencer"

Research Project

Project/Area Number 06558103
Research Category

Grant-in-Aid for Developmental Scientific Research (B)

Allocation TypeSingle-year Grants
Research Field Molecular biology
Research InstitutionKobe University

Principal Investigator

ISONO Katsumi  Kobe Univ., Faculty of Science Professor, 理学部, 教授 (70011640)

Co-Investigator(Kenkyū-buntansha) SAKURAI Toshiyuki  Hitachi Electronic Engineering, Engineer, 技術本部研究部, 技師
HONJOU Atsuko  Kobe Univ., Faculty of Science, Assistant, 理学部, 助手 (30229249)
KITAKAWA Madoka  Kobe Univ., Faculty of Science, Assistant, 理学部, 助手 (70169853)
Project Period (FY) 1994 – 1995
KeywordsTransposon / PCR / Magnetic beads / Nucleotide sequencing / Lambda phage / Base-caller / Control sequence database
Research Abstract

This project was aimed at establishing a method for more accurate and reliable base-calling system for the determination of nucleotide sequences using a DNA sequencer from Hitachi, model SQ3000. For this purpose, we obtained a large amount of nucleotide sequence raw data according to the transposon-facilitated PCR-based sequencing system of Kasai et al. (1992) using magnetic beads. As the template for analysis, we chose lambda phage DNA because of its easiness for preparation. We analyzed the distribution of peak distances and its dependence on the local nucleotide sequences and compared the sequence data obtained between electrophoresis lanes. The data were organized as a database and used for the probability calculation of individual nucleotides in the base-calling at each position of the sequence data. It thus turned out that the modified base-caller was more accurate in determining the sequence than the previous one : the accuracy level was at 97-100 % up to 300 bases and at 94-98 % up to 400 bases. Above 400 bases, however, the accuracy level was not very much improved by the new base-caller and it was found that other factors such as the quality of samples and acrylamide gel affected more on the base-calling accuracy.

  • Research Products

    (20 results)

All Other

All Publications (20 results)

  • [Publications] Grohman,L.: "The yeast MRP-L13 gene codes for a protein of the large subunit of the mitochondrial ribosome." Current Genetics. 26. 8-14 (1994)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Kasai,H.: "Use of trans-poson,PCR and magnetic beads for the genome analysis of E.coli K-12 : Further improvements of the method and analysis of the terC region." Proceedings of JBA Symposium on Microorganism DNA. 37-46 (1994)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Abe,R.: "Cloning and characterization of the ribosomal protein genes in the spc operon of a prokaryotic endosymbiont of the pea aphid,Acyrthosiphon kondoi." DNA Research. 1. 103-114 (1994)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Isono,K.: "Characteristic features of the nucleotide sequences of yeast mitochondrial ribosomal protein genes as analyzed by computer program GeneMark." DNA Research. 1. 263-269 (1994)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Moriya,H.: "Cloning and characterization of the hrpA gene in the terC region of Escherichia coli that is highly similar to the DEAH family RNA helicase genes of Saccharomyces cerevisiae." Nucleic Acids Research. 23. 595-598 (1995)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Hirosawa,M.: "Computer survey for likely genes in the one megabase contiguous genomic sequence data of Synechocystis sp.strain PCC6803." DNA Research. 2. 239-246 (1995)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Tanaka,S.: "Systematic mapping and characterization of ARS's of Saccharomycescerevisice chromosome V using a novel strategy." Yeast. 12. 101-113 (1996)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Berg,C.M.: "Transposon-facilitated large-scale DNA sequencing.In "Automated Sequencing and Analysis"" 51-59. (1994)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Kasai,H.: "Solid Phase Nucleotide Sequencing and Its Application to Genome Analysis of Escherichia coli K-12.In "Advances in Biomagnetic Separation"" 113-125. (1994)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Isono,K.: "Characterization of the genome of Saccharomyces cereviside and comparison with the genome of Candida albicans.In : Proceedings of the First International Symposium on DeepMycosis" (in press), (1996)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Berg, C.M., Wang, G., Isono, K., Kasai, H., Berg, D.E.: "Transposon-facilitated large-scale DNA sequencing. In "Automated Sequencing and Analysis"" Adams, M.D.et al.eds., Academic Press. 51-59 (1994)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Kasai, H., Kim, S.-O., Isono, S., Borodovsky, M., Isono, K.: "Solid Phase Nucleotide Sequencing and Its Application to Genome Analysis of Escherichia coli K-12. In "Advances in Biomagnetic Separation" Uhlen, M.et al.eds., Eaton Publishing. 113-125 (1994)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Grohman, L., Kitakawa, M., Isono, K., Goldschmidt-Reisin, S., Graack, H.-R.: "The yeast MRP-L13 gene codes for a protein of the large subunit of the mitochondrial ribosome." Curr.Genet.26. 8-14

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Kasai, H., Kim, S.-O., Isono, S., Moriya, H., Honjo, A., and Isono, K.: "Use of trans-poson, PCR and magnetic beads for the genome analysis of E.coli K-12 : Further improvements of the method and analysis of the terC region. Proceedings of JBA Symposium on Microorganism DNA" 37-46 (1994)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Abe, R., Yamashita, A., Isono, K.: "Cloning and characterization of the ribosomal protein genes in the spc operon of a prokaryotic endosymbiont of the pea aphid, Acyrthosiphon kondoi." DNA Research. 1. 103-114 (1994)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Isono, K., McIninch, J.D., Borodovsky, M.: "Characteristic features of the nucleotide sequences of yeast mitochondrial ribosomal protein genes as analyzed by computer program Gene Mark." DNA Res.1. 263-269 (1994)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Moriya, H., Kasai, H., Isono, K.: "Cloning and characterization of the hrpA gene in the terC region of Escherichia coli that is highly similar to the DEAH family RNA helicase genes of Saccharomyces cerevisiae" Nucl.Acids Res.23. 595-598 (1995)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Hirosawa, M., Kaneko, T., Tabata, S., McIninch, J.D., Hays, W.S., Borodovsky, M., Isono, K.: "Computer survey for likely genes in the one megabase contiguous genomic sequence data of of Synechocystis sp.strain PCC6803." DNA Res.2. 239-246 (1995)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Tanaka, S., Tanaka, Y., Isono, K.: "Systematic mapping and characterization of ARS's of Saccharomyces cerevisiae chromosome V using a novel strategy" Yeast. 12. 101-113 (1996)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Isono, K.: "Characterization of the genome of Saccharomyces cerevisiae and comparison with the genome of Candida albicans." In : Proceedings of the First International Symposium on Deep Mycosis. (in press). (1996)

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

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Published: 1997-03-04  

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