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. 2003 Jan 1;31(1):13-6.
doi: 10.1093/nar/gkg088.

DNA Data Bank of Japan (DDBJ) in XML

S Miyazaki  1 , H Sugawara, T Gojobori, Y Tateno
Affiliations

DNA Data Bank of Japan (DDBJ) in XML

S Miyazaki et al. Nucleic Acids Res. .

Abstract

The DNA Data Bank of Japan (DDBJ, http://www.ddbj.nig.ac.jp) has collected and released more entries and bases than last year. This is mainly due to large-scale submissions from Japanese sequencing teams on mouse, rice, chimpanzee, nematoda and other organisms. The contributions of DDBJ over the past year are 17.3% (entries) and 10.3% (bases) of the combined outputs of the International Nucleotide Sequence Databases (INSD). Our complete genome sequence database, Genome Information Broker (GIB), has been improved by incorporating XML. It is now possible to perform a more sophisticated database search against the new GIB than the ordinary BLAST or FASTA search.

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Figures

Figure 1
Figure 1
Top 10 species for which sequence data were submitted to DDBJ over the past year. Upper and lower figures respectively show the top 10 species in terms of the number of entries and that of bases. The vertical axis in the upper and lower figures respectively indicates the number of entries and that of bases. Number on the head of the bar indicates the exact number of entries or base for the species.
Figure 2
Figure 2
Query and the retrieval result in XML. This example shows a query written for searching for virulence and membrane in Escherichia coli K12W3110 and the result both in XML. Note that the result is itemized in terms of species, chromosome, feature, qualifier and so forth.
See this image and copyright information in PMC

References

    1. Watson J.D. and Crick,F.H.C. (1953) A structure for deoxyribose nucleic acids. Nature, 171, 737–738. - PubMed
    1. Maxam A.M. and Gilbert,W. (1977) A new method for sequencing DNA. Proc. Natl Acad. Sci. USA, 74, 560–564. - PMC - PubMed
    1. Sanger F., Nicklen,S. and Coulson,A.R. (1977) DNA sequencing with chain-terminating inhibitors. Proc. Natl Acad. Sci. USA, 74, 5463–5467. - PMC - PubMed
    1. Needlman S.B. and Wunsch,C.D. (1970) A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol., 48, 443–453. - PubMed
    1. Lipman D.J. and Pearson,W.R. (1985) Rapid and sensitive protein similarity searches. Science, 227, 1435–1441. - PubMed

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