NAR Molecular Biology Database Collection entry number 1

http://www.ddbj.nig.ac.jp

Imanishi, T.¹, Miyazaki, S.², Fukami-Kobayashi, K.², Sugawara, H.², Gojobori, T.², Tateno, Y.²

¹Japan Biological Information Research Center, National Institute of Advanced Industrial Science and Technology, Aomi, Koto-ku, Tokyo 135-0064, Japan
²Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Yata, Mishima 411-8540, Japan

Contact ytateno@genes.nig.ac.jp

With the advent of genome biology and sequencing technology DNA sequence data had been produced at an enormous rate, and at last the human genome was almost completely sequenced and immediately published in Nature (1) and the International Nucleotide Sequence Databases (INSD) in 2001. The immediate public release of such a large- scale sequence data was possible perhaps only through INSD. Since INSD was composed of the DNA Data Bank of Japan (DDBJ, http://www.ddbj.nig.ac.jp), the EMBL Bank and GenBank, the publication of the human genome data was carried out smoothly on the basis of a well-established international collaboration. As a result, a number of researchers enjoyed worldwide the simultaneous publications of the Nature paper and the relevant sequence data. By use of the DNA data and retrieval and analysis tools available at DDBJ one can push ahead with one's research in various areas of life sciences. With this in mind we at DDBJ have made an effort in collecting as much data as possible mainly from Japanese researchers. The increase rate of the data we collected, annotated and released to the public in the past year is 1.6 times in the number of entries and 1.5 times in the number of bases. The increase rate is being accelerated even after the human genome was sequenced, because sequencing technology has been remarkably advanced and simplified, and research in life sciences has been shifted from the gene

To extend our annotation capacity further, we have developed the Genome Information Broker (GIB, http://gib.genes.ac.jp) (2) that now includes more than 50 complete microbial genome data and Arabidopsis genome data. GIB enables one to carry out various genome-wide retrievals not only for one species but also across all the included species. GIB may particularly be used for the study of genome evolution. We have also developed a database of the human genome, the Human Genome Studio (HGS, http://studio.nig.ac.jp). HGS provides one with a set of sequences being as continuous as possible in any one of the 24 chromosomes. HGS is also equipped with a simple retrieval tool. Both GIB and HGS have been updated incorporating newly available data and retrieval

We thank the rest of the DDBJ members for making it possible to run this international DNA data bank. We are also grateful to the Ministry of Education, Science, Culture, Sports and Technology for their financial support

1. International Human Genome Sequencing Consortium. (2001) Initial sequencing and analysis of the human genome. Nature 409, 860-921.
2. Tateno, Y., Fukami-Kobayashi, K., Miyazaki, S., Sugawara, H., Gojobori, T. (1998) DNA Data Bank of Japan at work on genome sequence data. Nucleic Acids Research 26, 16-20.

Go to the abstract in the NAR 2008 Database Issue.

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