What is DDBJ?

DDBJ; DNA Data Bank of Japan is the sole nucleotide sequence data bank in Asia, which is officially certified to collect nucleotide sequences from researchers and to issue the internationally recognized accession number to data submitters.Since we exchange the collected data with EMBL-Bank/EBI; European Bioinformatics Institute and GenBank/NCBI; National Center for Biotechnology Information on a daily basis, the three data banks 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 number to researchers in any other countries.

DDBJ is organized by NIG; National Institute of Genetics with endorsement of MEXT; Japanese Ministry of Education, Culture, Sports, Science and Technology. 99% of INSD data from Japanese researchers are submitted through DDBJ.

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 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.

In detail, following items about DDBJ are briefly explained.

International Collaboration Framework of Nucleotide Sequence Database Construction

Governing Structure of DDBJ

Major Activities of DDBJ

International Collaboration Framework of Nucleotide Sequence Database Construction

From the beginning, DDBJ has been functioning as one of the international nucleotide sequence databases, including EMBL-Bank/EBI in Europe and GenBank/NCBI in the USA as the two other members.

DDBJ/EMBL-Bank/GenBank collects the nucleotide sequence data experimentally determined, and constructs the database in accordance with the rule agreed with the three data banks (i.e. (Feature Table: Definition and agreements in International Collaborative Meeting).

The database is a collection of "entry" which is the unit of the data. Each entry includes nucleotide sequence and the information of submitters, references, source organisms, and the biological nature such as gene function and other property of the sequence, etc.

The database also includes the data from Japan Patent Office (JPO), European Patent Office (EPO), United States Patent and Trademark Office (USPTO), and Korean Intellectual Property Office (KIPO).

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.

Consequently, we have been collaborating with the two data banks through exchanging data and information on internet and by regularly holding two meetings, the International Advisory Committee and the International Collaborative Meeting.The operations of DDBJ/EMBL-Bank/GenBank and ICM subscribe to advice from IAC.

IAC; International Advisory Committee

International Advisory Committee consists of nine members, each of 3 members selected from Europe, US, or Japan.The committee meeting to advice in fairness to maintenance and future plan of INSDC is held once a year.

ICM; International Collaborative Meeting

International Collaborative Meeting consists of working-level participants of INSDC and its fundamental principle is international collaboration.The meeting to discuss practical matters to maintain and update INSDC is held once a year.

INSDC; International Nucleotide Sequence Database Collaboration

In 2005, 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".
The agreement was approved by IAC in May 2005.

In 2009, INSDC added a coraborative meeting to deal with mass sequence data produced by the "next" generation sequencers (Sequence Read Archive) and traces produced by traditional sequencers (Trace Archive).

In 2010, ENA; European Nucleotide Archive was reorganized at EBI.

A schematic view of INSDC is shown below.

Governing Structure of DDBJ

Currently, DDBJ is in operation at the National Institute of Genetics in Mishima, Japan.

Faculty Staff of DDBJ

DDBJ began data bank activities in earnest in 1986 at NIG with the endorsement of the Ministry of Education, Science, Sport and Culture.
To operate DDBJ more efficiently, CIB; the Center for Information Biology was established in NIG in 1995.
CIB was reorganized as CIB-DDBJ; the Center for Information Biology and DNA Data Bank of Japan in 2001.
CIB-DDBJ was to play a major role in carrying out research in information biology and to run DDBJ operation in the world.
It is generally accepted that research in biology today requires both computer and experimental equipment equally well.
In particular, we 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.

In April 2004, NIG was reorganized as a member of ROIS; Research Organization of Information and Systems. DDBJ has also belonged to ROIS.

DBCLS; Database Center for Life Science was newly founded in ROIS in April 2007.

In 2009, DDBJ faculty staff have greatly been reshuffled. DDBJ collaborates with DBCLS more closely.

In 2012, DDBJ, expanding its DNA databank activities, was restructured as one of the Intellectual Infrastructure Project Centers of NIG, being separated from CIB.

1. One of the members of INSDC

2. Bioinformatics databases management

3. Developing software tools for analyzing biological data

4. Holding a course to teach begineners: How to analyze biological data

1. One of the members of INSDC

DDBJ is officially certified to collect nucleotide sequences from researchers and to issue the internationally recognized accession number to data submitters.Since DDBJ exchanges the collected data with EMBL-Bank and GenBank on a daily basis, the three data banks share virtually the same data at any given time.

See following links in detail.

Nucleotide Sequence Submission
Current Scheme of the Sequence Data Transition
Collective Download from FTP site
Search and Analysis of sequence data

2. Bioinformatics databases management: tools for depositing and retrieving

Our databases and sequence retrieval tools have greatly contributed to the paradigm shift in biology. Biology or life sciences are no longer restricted to wet-bentch experiments. In silico and in vitro / in vivo analyses together will push back the frontiers of life sciences.

See following links in detail about databases provided and maintained by at DDBJ and others.

All-round Retrieval of Sequence and Annotation (ARSA)
Search and Analysis
collective download from FTP site

3. Developing software tools for analyzing biological data

We also provide many tools for data analyses developed by at DDBJ and others.

See following links in detail.

Web API for Biology (WABI)    ※suspended
Search and Analysis

4. Holding a course to teach begineners: How to analyze biological data

DDBJ holds a course Bioinformatics Training Course (in Japanese), to teach how to analyze biological data.

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DNA Data Bank of Japan (DDBJ)

Postal Address:
National Institute of Genetics
1111 Yata, Mishima, 411-8540, Japan
Fax: +81-55-981-6849

Contact US for

Data Submission
Updating Submitted Data
SAKURA Support
Mass Submission
DDBJ BioProject Database
DDBJ Sequence Read Archive/DDBJ Trace Archive
Web Support (getentry, ARSA, BLAST, ClustalW, etc)
Super Computer System
DDBJ General Information