Skip to main content
NCBI home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1998 Jan 1;26(1):16–20. doi: 10.1093/nar/26.1.16

DNA Data Bank of Japan at work on genome sequence data.

Y Tateno 1, K Fukami-Kobayashi 1, S Miyazaki 1, H Sugawara 1, T Gojobori 1
PMCID: PMC147185  PMID: 9399792

Abstract

We at the DNA Data Bank of Japan (DDBJ) (http://www.ddbj.nig.ac.jp) have recently begun receiving, processing and releasing EST and genome sequence data submitted by various Japanese genome projects. The data include those for human, Arabidopsis thaliana, rice, nematode, Synechocystis sp. and Escherichia coli. Since the quantity of data is very large, we organized teams to conduct preliminary discussions with project teams about data submission and handling for release to the public. We also developed a mass submission tool to cope with a large quantity of data. In addition, to provide genome data on WWW, we developed a genome information system using Java. This system (http://mol.genes.nig.ac.jp/ecoli/) can in theory be used for any genome sequence data. These activities will facilitate processing of large quantities of EST and genome data.

Full Text

The Full Text of this article is available as a PDF (3.4 MB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Adams M. D., Kelley J. M., Gocayne J. D., Dubnick M., Polymeropoulos M. H., Xiao H., Merril C. R., Wu A., Olde B., Moreno R. F. Complementary DNA sequencing: expressed sequence tags and human genome project. Science. 1991 Jun 21;252(5013):1651–1656. doi: 10.1126/science.2047873. [DOI] [PubMed] [Google Scholar]
  2. Aiba H., Baba T., Hayashi K., Inada T., Isono K., Itoh T., Kasai H., Kashimoto K., Kimura S., Kitakawa M. A 570-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 28.0-40.1 min region on the linkage map. DNA Res. 1996 Dec 31;3(6):363–377. doi: 10.1093/dnares/3.6.363. [DOI] [PubMed] [Google Scholar]
  3. Altschul S. F., Gish W., Miller W., Myers E. W., Lipman D. J. Basic local alignment search tool. J Mol Biol. 1990 Oct 5;215(3):403–410. doi: 10.1016/S0022-2836(05)80360-2. [DOI] [PubMed] [Google Scholar]
  4. Blattner F. R., Plunkett G., 3rd, Bloch C. A., Perna N. T., Burland V., Riley M., Collado-Vides J., Glasner J. D., Rode C. K., Mayhew G. F. The complete genome sequence of Escherichia coli K-12. Science. 1997 Sep 5;277(5331):1453–1462. doi: 10.1126/science.277.5331.1453. [DOI] [PubMed] [Google Scholar]
  5. Bult C. J., White O., Olsen G. J., Zhou L., Fleischmann R. D., Sutton G. G., Blake J. A., FitzGerald L. M., Clayton R. A., Gocayne J. D. Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii. Science. 1996 Aug 23;273(5278):1058–1073. doi: 10.1126/science.273.5278.1058. [DOI] [PubMed] [Google Scholar]
  6. Butler D. Funding assured for international malaria sequencing project. Nature. 1997 Aug 21;388(6644):701–701. doi: 10.1038/41826. [DOI] [PubMed] [Google Scholar]
  7. Cantor C. R. Orchestrating the Human Genome Project. Science. 1990 Apr 6;248(4951):49–51. doi: 10.1126/science.2181666. [DOI] [PubMed] [Google Scholar]
  8. Dulbecco R. A turning point in cancer research: sequencing the human genome. Science. 1986 Mar 7;231(4742):1055–1056. doi: 10.1126/science.3945817. [DOI] [PubMed] [Google Scholar]
  9. Eki T., Abe M., Naitou M., Sasanuma S. I., Nohata J., Kawashima K., Ahmad I., Hanaoka F., Murakami Y. Cloning and characterization of novel gene, DCRR1, expressed from Down's syndrome critical region of human chromosome 21q22.2. DNA Seq. 1997;7(3-4):153–164. doi: 10.3109/10425179709034031. [DOI] [PubMed] [Google Scholar]
  10. Fleischmann R. D., Adams M. D., White O., Clayton R. A., Kirkness E. F., Kerlavage A. R., Bult C. J., Tomb J. F., Dougherty B. A., Merrick J. M. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science. 1995 Jul 28;269(5223):496–512. doi: 10.1126/science.7542800. [DOI] [PubMed] [Google Scholar]
  11. Fraser C. M., Gocayne J. D., White O., Adams M. D., Clayton R. A., Fleischmann R. D., Bult C. J., Kerlavage A. R., Sutton G., Kelley J. M. The minimal gene complement of Mycoplasma genitalium. Science. 1995 Oct 20;270(5235):397–403. doi: 10.1126/science.270.5235.397. [DOI] [PubMed] [Google Scholar]
  12. Gish W., States D. J. Identification of protein coding regions by database similarity search. Nat Genet. 1993 Mar;3(3):266–272. doi: 10.1038/ng0393-266. [DOI] [PubMed] [Google Scholar]
  13. Goffeau A., Barrell B. G., Bussey H., Davis R. W., Dujon B., Feldmann H., Galibert F., Hoheisel J. D., Jacq C., Johnston M. Life with 6000 genes. Science. 1996 Oct 25;274(5287):546, 563-7. doi: 10.1126/science.274.5287.546. [DOI] [PubMed] [Google Scholar]
  14. Hawkins T. L., McKernan K. J., Jacotot L. B., MacKenzie J. B., Richardson P. M., Lander E. S. A magnetic attraction to high-throughput genomics. Science. 1997 Jun 20;276(5320):1887–1889. doi: 10.1126/science.276.5320.1887. [DOI] [PubMed] [Google Scholar]
  15. Himmelreich R., Hilbert H., Plagens H., Pirkl E., Li B. C., Herrmann R. Complete sequence analysis of the genome of the bacterium Mycoplasma pneumoniae. Nucleic Acids Res. 1996 Nov 15;24(22):4420–4449. doi: 10.1093/nar/24.22.4420. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Kaneko T., Sato S., Kotani H., Tanaka A., Asamizu E., Nakamura Y., Miyajima N., Hirosawa M., Sugiura M., Sasamoto S. Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. strain PCC6803. II. Sequence determination of the entire genome and assignment of potential protein-coding regions. DNA Res. 1996 Jun 30;3(3):109–136. doi: 10.1093/dnares/3.3.109. [DOI] [PubMed] [Google Scholar]
  17. Maxam A. M., Gilbert W. A new method for sequencing DNA. Proc Natl Acad Sci U S A. 1977 Feb;74(2):560–564. doi: 10.1073/pnas.74.2.560. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Murakami Y., Naitou M., Hagiwara H., Shibata T., Ozawa M., Sasanuma S., Sasanuma M., Tsuchiya Y., Soeda E., Yokoyama K. Analysis of the nucleotide sequence of chromosome VI from Saccharomyces cerevisiae. Nat Genet. 1995 Jul;10(3):261–268. doi: 10.1038/ng0795-261. [DOI] [PubMed] [Google Scholar]
  19. O'Brien C. Entire E. coli genome sequenced -- at last. Nature. 1997 Feb 6;385(6616):472–472. doi: 10.1038/385472a0. [DOI] [PubMed] [Google Scholar]
  20. Ohira M., Ichikawa H., Suzuki E., Iwaki M., Suzuki K., Saito-Ohara F., Ikeuchi T., Chumakov I., Tanahashi H., Tashiro K. A 1.6-Mb P1-based physical map of the Down syndrome region on chromosome 21. Genomics. 1996 Apr 1;33(1):65–74. doi: 10.1006/geno.1996.0160. [DOI] [PubMed] [Google Scholar]
  21. Ohira M., Ootsuyama A., Suzuki E., Ichikawa H., Seki N., Nagase T., Nomura N., Ohki M. Identification of a novel human gene containing the tetratricopeptide repeat domain from the Down syndrome region of chromosome 21. DNA Res. 1996 Feb 29;3(1):9–16. doi: 10.1093/dnares/3.1.9. [DOI] [PubMed] [Google Scholar]
  22. Olson M., Hood L., Cantor C., Botstein D. A common language for physical mapping of the human genome. Science. 1989 Sep 29;245(4925):1434–1435. doi: 10.1126/science.2781285. [DOI] [PubMed] [Google Scholar]
  23. Report and abstracts of the Fifth International Workshop on Human Chromosome 21 Mapping 1994. Tsukuba, Japan, November 9-11, 1994. Cytogenet Cell Genet. 1995;70(3-4):147–182. doi: 10.1159/000134027. [DOI] [PubMed] [Google Scholar]
  24. Sanger F., Nicklen S., Coulson A. R. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A. 1977 Dec;74(12):5463–5467. doi: 10.1073/pnas.74.12.5463. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Tomb J. F., White O., Kerlavage A. R., Clayton R. A., Sutton G. G., Fleischmann R. D., Ketchum K. A., Klenk H. P., Gill S., Dougherty B. A. The complete genome sequence of the gastric pathogen Helicobacter pylori. Nature. 1997 Aug 7;388(6642):539–547. doi: 10.1038/41483. [DOI] [PubMed] [Google Scholar]
  26. Venter J. C., Smith H. O., Hood L. A new strategy for genome sequencing. Nature. 1996 May 30;381(6581):364–366. doi: 10.1038/381364a0. [DOI] [PubMed] [Google Scholar]
  27. Watanabe H., Mori H., Itoh T., Gojobori T. Genome plasticity as a paradigm of eubacteria evolution. J Mol Evol. 1997;44 (Suppl 1):S57–S64. doi: 10.1007/pl00000052. [DOI] [PubMed] [Google Scholar]
  28. Wolfe K. H., Shields D. C. Molecular evidence for an ancient duplication of the entire yeast genome. Nature. 1997 Jun 12;387(6634):708–713. doi: 10.1038/42711. [DOI] [PubMed] [Google Scholar]

Articles from Nucleic Acids Research are provided here courtesy of Oxford University Press

RESOURCES