DDBJ Center collects nucleotide sequence data as a member of INSDC (International Nucleotide Sequence Database Collaboration) and provides freely available nucleotide sequence data and supercomputer system, to support research activities in life science.
It is generally accepted that research in biology today requires both computer and experimental equipment equally well. Information achieved from enormous exhaustive data have greatly contributed to the paradigm shift in biology. Biology or life sciences are no longer restricted to wet-bench experiments. In silico and in vitro / in vivo analyses together will push back the frontiers of life sciences. In particular, researchers in life science must rely on computers to analyze nucleotide sequence data accumulating at a remarkably rapid rate. Actually, this triggered the birth and development of information biology. DDBJ Center is to play a major role in carrying out research in information biology and to run DDBJ operation in the world.
The principal purpose of DDBJ operations is to improve the quality of INSD, as public domains. When researchers make their data open to the public through INSD and commonly shared in world wide, we at DDBJ Center make efforts to describe information on the data as rich as possible, according to the unified rules of INSD, preferably without any stress by using DDBJ.
Nucleotide sequence records organismic evolution more directly than other biological materials and thus is invaluable not only for research in life sciences but also human welfare in general. The database is, so to speak, a common treasure of human beings. With this in mind, we make the database online accessible to anyone in the world.
Currently, DDBJ Center is in operation at Research Organization of Information and System National Institute of Genetics(NIG) in Mishima, Japan with endorsement of MEXT; Japanese Ministry of Education, Culture, Sports, Science and Technology.
DDBJ Center is reviewed and advised by its own advisory board, DNA Database Advisory Committee (an outside committee of NIG), and also by the advisory board to INSDC, International Advisory Committee.
Construction and Operation of INSDC
DDBJ Center is officially certified to collect nucleotide sequences from researchers and to issue the internationally recognized accession number to data submitters. The accession number issued for each sequence data is unique on the database and internationally recognized to guarantee the submitter the property of the submitted and published data. Since DDBJ Center exchanges the released data with ENA/EBI and NCBI on a daily basis, the three data centers share virtually the same data at any given time. The virtually unified database is called INSD; International Nucleotide Sequence Database.
DDBJ collects sequence data mainly from Japanese researchers, but of course accepts data and issue the accession numbers to researchers in any other countries. 99% of INSD data from Japanese researchers are submitted through DDBJ.
Providing nucleotide and amino acid sequence data related to patent applications
INSD contains nucleotide sequence data related to patent applications collected by Patent Offices in Japan, Korea, Europe and USA.
DDBJ Center also provides amino acid sequence data related to patent applications collected by patent offices in Japan and Korea. See following links in detail.
Management and operation of the National Institute of Genetics Supercomputer System
The National Institute of Genetics Supercomputer System (NIG Supercomputer) is a large-scale computer utilization site with genome analysis as its primary focus. The system provides Supercomputing System Services comprising leading-edge, large-scale cluster-type computers, large-scale memory-sharing computers, and high-capacity, high-speed disk devices.
Providing services to search and to analyze biological data
Biological database management: tools for depositing and retrieving
Providing software tools for analyzing biological data
We provide software tools for data analyses developed by DDBJ and others through web services or on NIG Supercomputer.
Training course and publication
DDBJ holds a training course for bioinformatics, DDBJing (in Japanese), to teach how to submit nucleotide sequence data and how to use our services for analyzing life science data.
- EMBL data library was organized, and asked international cooperation for nucleotide sequence data bank to Japan.
- EMBL and GenBank started international cooperation, and invited Japan to participate their data bank.
- Aimed at contribution for international data bank to collect, to evaluate and to provide nucleotide sequence data, trial data loading was started.
- NIG; the National Institute of Genetics was reorganized as an Inter-University Research Institute.
DDBJ began to work at NIG.
- DNA Database Advisory Committee organized.
- DDBJ release 1 was provided.
By this release, we regard this year as official start of DDBJ operation.
- To operate DDBJ more efficiently, CIB; the Center for Information Biology was established in NIG.
- CIB was reorganized as CIB-DDBJ; the Center for Information Biology and DNA Data Bank of Japan
- NIG was reorganized as a member of ROIS; Research Organization of Information and Systems. DDBJ has also belonged to ROIS.
- DDBJ, EMBL-Bank and GenBank agreed to call their collaboration INSDC; International Nucleotide Sequence Database Collaboration; and to call the unified nucleotide sequence database INSD; the International Nucleotide Sequence Database.
- DBCLS; Database Center for Life Science was newly founded in ROIS
- DDBJ faculty staff have greatly been reshuffled. DDBJ collaborates with DBCLS more closely.
INSDC added a collaborative meeting to deal with huge sequence data produced by the next generation sequencers (Sequence Read Archive) and traces produced by traditional sequencers (Trace Archive).
- DDBJ, expanding its DNA databank activities, was restructured as one of the Intellectual Infrastructure Project Centers of NIG, being separated from CIB.