DNA Data Bank of Japan

Sequences of the genes/cDNAs can be retrieved from databases on the Internet at various web sites. For example, GeneBank (at the National Center for Biotechnology Information, NCBI) is at http //www.ncbi.nlm.nih.gov/ Web/Search/index.html. The EMBL Nucleotide Sequence database (through the European Bioinformatic Institute, EBI) can be found at http //www.ebi.ac.uk/queries/queries.html, whilst that of the DNA Data Bank of Japan is at http //www.ddbj.nig.ac.jp/. 

DDJB (http //www.ddbj.nig.ac.jp/), DNA Data Bank of Japan. 

The sequence data is compared to one or more of a proprietary (Microseq) or public (GenBank, http //www.ncbi.nlm.nih.gov EMBL Nucleotide Sequence Databank, http //www.ebi.ac.uk/embl/ DNA Data Bank of Japan (DDBJ), http //www.ddbj.nig.ac.jp/) database for identification. Frequently, only a portion of the gene, such as the internal transcribed spacer (ITS) regions, especially the ITSl region of SSU rDNAl 30>55.56,58,59 variable D2 region of the LSU rDNA,l >53... 

DDBJ (Tateno et al, 2002) is the DNA Data Bank of Japan in collaboration with GenBank and EMBL. The database is produced, maintained, and distributed at the National Institute of Genetics. The entry of DDBJ follows the keywords adapted by the GenBank. 

The nucleotide sequences can be retrieved from one of the three IC (International Collaboration) nucleotide sequence repositories/databases GenBank, EMBL Nucleotide Sequence Database, and DNA Data Bank of Japan (DDBJ). The retrieval can be conducted via accession numbers or keywords. Keynet (http // www.ba.cnr.it/keynet.html) is a tree browsing database of keywords extracted from... 

Field/value-based flat files have been very commonly used in bioinformatics. Examples are the flat file libraries from GenBank, European Molecular Biology Laboratory Nucleotide Sequence Database (EMBL), DNA Data Bank of Japan, or Universal Protein Resource (UniProt). These file types are a very limited solution because they lack referencing, vocabulary control, and constraints. In addition, on the file level, there is no inherent locking mechanism that detects when a file is being used or modified. However, these file types are primarily used for reading purposes. 

Tateno, Y, Miyazaki, S., Ota, M., Sugawara, H., and Gojobori, T. (1997). DNA Data Bank of Japan (DDBJ) in collaboration with mass sequencing teams. Nucl. Acids Res. 28, 24-26. 

The DNA Data Bank of Japan (http //www.genome.ad.jp/) is a Japanese network of database and computational service for genome research and related areas in molecular and cellular biology (Tateno et al, 2005). It is operated jointly by the Institute for Chemical Research, Kyoto University and the Human Genome Center of the University of Tokyo. 

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