Lecture 10 - DNA Data Bank of Japan (DDBJ) – Introduction | Bioinformatics - Botany PDF Download

 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