Page 1
DDBJ-Introduction
Institute of Lifelong Learning, University of Delhi
Subject: Bioinformatic
Lesson: DNA Data Bank of Japan (DDBJ)
Lesson Developer: Jasmeet Kaur Abat
College/ Department: Department of Botany, Gargi College,
University of Delhi
Page 2
DDBJ-Introduction
Institute of Lifelong Learning, University of Delhi
Subject: Bioinformatic
Lesson: DNA Data Bank of Japan (DDBJ)
Lesson Developer: Jasmeet Kaur Abat
College/ Department: Department of Botany, Gargi College,
University of Delhi
DDBJ- Introduction
Institute of Lifelong Learning, University of Delhi 1
Table of Contents
Chapter: DNA Databank of Japan (DDBJ)
? Introduction
? History
? Functions of DDBJ
? Activities of DDBJ
? Collection of sequences
? Tools for data retrieval
? Software development
? Training courses
? Sequence submission
? Nucleotide Sequence Submission system
? Mass Submission System
? Data Updates
? DDBJ Sequence Read Archives
? DDBJ Trace Archives
? BioProject Database
? Database Services
? DDBJ Omics Archive
? DDBJ Read Annotation Pipeline
? Summary
? Exercise/ Practice
? Glossary
? References/ Bibliography/ Further Reading
Page 3
DDBJ-Introduction
Institute of Lifelong Learning, University of Delhi
Subject: Bioinformatic
Lesson: DNA Data Bank of Japan (DDBJ)
Lesson Developer: Jasmeet Kaur Abat
College/ Department: Department of Botany, Gargi College,
University of Delhi
DDBJ- Introduction
Institute of Lifelong Learning, University of Delhi 1
Table of Contents
Chapter: DNA Databank of Japan (DDBJ)
? Introduction
? History
? Functions of DDBJ
? Activities of DDBJ
? Collection of sequences
? Tools for data retrieval
? Software development
? Training courses
? Sequence submission
? Nucleotide Sequence Submission system
? Mass Submission System
? Data Updates
? DDBJ Sequence Read Archives
? DDBJ Trace Archives
? BioProject Database
? Database Services
? DDBJ Omics Archive
? DDBJ Read Annotation Pipeline
? Summary
? Exercise/ Practice
? Glossary
? References/ Bibliography/ Further Reading
DDBJ- Introduction
Institute of Lifelong Learning, University of Delhi 2
Introduction
Databases are like information banks which are used for storing and retrieval of sequence
information. DNA Databank of Japan (DDBJ; http://www.ddbj.nig.ac.jp) is one of three
nucleotide database which together with National Center for Biotechnology Information
(NCBI) and European Bioinformatics Institute (EMBL), form a consortium known as
International Nucleotide Sequence Database Collaboration (INSDC). DDBJ is the only
nucleotide sequence databank of Asian origin and mainly collects sequences from Japanese
researches. It is a primary nucleotide database; it collects data directly from the
researchers. On accepting a nucleotide sequence, DDBJ issues an accession number to the
submitter which has an international recognition. From July 2011 and June 2012, DDBJ had
collected and released 15243000 entries/ 12270462217 bases (Ogasawara et al., 2012).
During 2009-10 DDBJ contributed 25.4% of the entries and 21.5% of the bases added to
INSDC (Kaminuma et al., 2011).
Figure : Homepage of DDBJ database. The figure shows various resources and tools
available at DDBJ.
Source: http://www.ddbj.nig.ac.jp/
Page 4
DDBJ-Introduction
Institute of Lifelong Learning, University of Delhi
Subject: Bioinformatic
Lesson: DNA Data Bank of Japan (DDBJ)
Lesson Developer: Jasmeet Kaur Abat
College/ Department: Department of Botany, Gargi College,
University of Delhi
DDBJ- Introduction
Institute of Lifelong Learning, University of Delhi 1
Table of Contents
Chapter: DNA Databank of Japan (DDBJ)
? Introduction
? History
? Functions of DDBJ
? Activities of DDBJ
? Collection of sequences
? Tools for data retrieval
? Software development
? Training courses
? Sequence submission
? Nucleotide Sequence Submission system
? Mass Submission System
? Data Updates
? DDBJ Sequence Read Archives
? DDBJ Trace Archives
? BioProject Database
? Database Services
? DDBJ Omics Archive
? DDBJ Read Annotation Pipeline
? Summary
? Exercise/ Practice
? Glossary
? References/ Bibliography/ Further Reading
DDBJ- Introduction
Institute of Lifelong Learning, University of Delhi 2
Introduction
Databases are like information banks which are used for storing and retrieval of sequence
information. DNA Databank of Japan (DDBJ; http://www.ddbj.nig.ac.jp) is one of three
nucleotide database which together with National Center for Biotechnology Information
(NCBI) and European Bioinformatics Institute (EMBL), form a consortium known as
International Nucleotide Sequence Database Collaboration (INSDC). DDBJ is the only
nucleotide sequence databank of Asian origin and mainly collects sequences from Japanese
researches. It is a primary nucleotide database; it collects data directly from the
researchers. On accepting a nucleotide sequence, DDBJ issues an accession number to the
submitter which has an international recognition. From July 2011 and June 2012, DDBJ had
collected and released 15243000 entries/ 12270462217 bases (Ogasawara et al., 2012).
During 2009-10 DDBJ contributed 25.4% of the entries and 21.5% of the bases added to
INSDC (Kaminuma et al., 2011).
Figure : Homepage of DDBJ database. The figure shows various resources and tools
available at DDBJ.
Source: http://www.ddbj.nig.ac.jp/
DDBJ- Introduction
Institute of Lifelong Learning, University of Delhi 3
History
DDBJ was established in the year 1986 at the National Institute of Genetics (NIG), Japan
with support from the Japanese Ministry of Education, Culture, Sports, Science and
Technology (MEXT). Later on for its efficient functioning, Center for Information Biology
(CIB) was established at NIG in 1995. In 2004, NIG was made a member of Research
Organization of Information and Systems.
The functioning and maintenance of DDBJ is monitored by an international advisory
committee consisting of 9 members from Japan, Europe and USA. The committee reviews
the functioning of DDBJ and reports the progress of DDBJ in database issue of Nucleic Acid
Research Journal every year. Since its inception there has been a tremendous increase in
the number of sequences submitted to DDBJ .
Page 5
DDBJ-Introduction
Institute of Lifelong Learning, University of Delhi
Subject: Bioinformatic
Lesson: DNA Data Bank of Japan (DDBJ)
Lesson Developer: Jasmeet Kaur Abat
College/ Department: Department of Botany, Gargi College,
University of Delhi
DDBJ- Introduction
Institute of Lifelong Learning, University of Delhi 1
Table of Contents
Chapter: DNA Databank of Japan (DDBJ)
? Introduction
? History
? Functions of DDBJ
? Activities of DDBJ
? Collection of sequences
? Tools for data retrieval
? Software development
? Training courses
? Sequence submission
? Nucleotide Sequence Submission system
? Mass Submission System
? Data Updates
? DDBJ Sequence Read Archives
? DDBJ Trace Archives
? BioProject Database
? Database Services
? DDBJ Omics Archive
? DDBJ Read Annotation Pipeline
? Summary
? Exercise/ Practice
? Glossary
? References/ Bibliography/ Further Reading
DDBJ- Introduction
Institute of Lifelong Learning, University of Delhi 2
Introduction
Databases are like information banks which are used for storing and retrieval of sequence
information. DNA Databank of Japan (DDBJ; http://www.ddbj.nig.ac.jp) is one of three
nucleotide database which together with National Center for Biotechnology Information
(NCBI) and European Bioinformatics Institute (EMBL), form a consortium known as
International Nucleotide Sequence Database Collaboration (INSDC). DDBJ is the only
nucleotide sequence databank of Asian origin and mainly collects sequences from Japanese
researches. It is a primary nucleotide database; it collects data directly from the
researchers. On accepting a nucleotide sequence, DDBJ issues an accession number to the
submitter which has an international recognition. From July 2011 and June 2012, DDBJ had
collected and released 15243000 entries/ 12270462217 bases (Ogasawara et al., 2012).
During 2009-10 DDBJ contributed 25.4% of the entries and 21.5% of the bases added to
INSDC (Kaminuma et al., 2011).
Figure : Homepage of DDBJ database. The figure shows various resources and tools
available at DDBJ.
Source: http://www.ddbj.nig.ac.jp/
DDBJ- Introduction
Institute of Lifelong Learning, University of Delhi 3
History
DDBJ was established in the year 1986 at the National Institute of Genetics (NIG), Japan
with support from the Japanese Ministry of Education, Culture, Sports, Science and
Technology (MEXT). Later on for its efficient functioning, Center for Information Biology
(CIB) was established at NIG in 1995. In 2004, NIG was made a member of Research
Organization of Information and Systems.
The functioning and maintenance of DDBJ is monitored by an international advisory
committee consisting of 9 members from Japan, Europe and USA. The committee reviews
the functioning of DDBJ and reports the progress of DDBJ in database issue of Nucleic Acid
Research Journal every year. Since its inception there has been a tremendous increase in
the number of sequences submitted to DDBJ .
DDBJ- Introduction
Institute of Lifelong Learning, University of Delhi 4
Figure : Growth of DDBJ/EMBL/NCBI in terms of nucleotide data submitted over the years.
Source: http://www.ddbj.nig.ac.jp/breakdown_stats/dbgrowth-e.html
Roles of DDBJ
As a member of INSDC, primary objective of DDBJ is to collect sequence data from
researchers all over the world and to issue a unique accession number for each entry. The
data collected from the submitters is made publically available and anyone can access the
data through data retrieval tools available at DDBJ. Everyday data submitted at either DDBJ
or EMBL or NCBI is exchanged, therefore at any given time these three databases contain
same data .
Figure: Diagrammatic representation of data exchange between DDBJ/NCBI/EMBL on daily
basis. These three databases together form a collaboration called as INSDC.
Source: Dr Jasmeet Abat
Activities of DDBJ
Following are the activities of DDBJ:
Collection of sequences
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