Databases DDBJ, NCBI, EMBL

1. DDBJ, NCBI, EMBL

2.  DDBJ (DNA Data Bank of Japan) (DDBJ,
http://www.ddbj.nig.ac.jp)
 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.

3.  The DNA Data Bank of Japan (DDBJ) is located at the National Institute
of Genetics (NIG) in the Shizuoka prefecture of Japan. It is also a
member of the International Nucleotide Sequence Database
Collaboration (INSDC). It exchanges its data with European Molecular
Biology Laboratory at the European Bioinformatics Institute and with
GenBank at the National Center for Biotechnology Information on a
daily basis. Thus these three databanks contain the same data at any
given time.
 DDBJ began data bank activities in 1986 at NIG and remains the only
nucleotide sequence data bank in Asia. Although DDBJ mainly receives
its data from Japanese researchers, it can accept data from
contributors from any other country. DDBJ is primarily funded by the
Japanese Ministry of Education, Culture, Sports, Science and
Technology (MEXT). DDBJ has an international advisory committee
which consists of nine members, 3 members each from Europe, US,
and Japan. This committee advises DDBJ about its maintenance,
management and future plans once a year. Apart from this DDBJ also
has an international collaborative committee which advises on various
technical issues related to international collaboration and consists of

12. Accession
number
organism
Author’s
reference
Nucleotide
sequence

15.  The submission of data to DDBJ follows a
specific workflow
1. Submission of Data: In general, DDBJ
accepts submissions of nucleotide
sequences through the Nucleotide
Sequence Submission System or the Mass
Submission System. After processing
submitted data, DDBJ assigns accession
number to each sequence.
Submission can be done by two methods
 a. Nucleotide Sequence Submission System
 b. Mass Submission System or MSS

16. a. Nucleotide Sequence Submission System
DDBJ suggests that you use the Nucleotide
Sequence Submission System in general.
b. Mass Submission System or MSS: The MSS
is recommended only if submission contains
an increased number of sequences (>1024),
long nucleotide sequences or it contains
multiple features (>30 in an entry).

19. 2. Annotation: Annotation is performed in
compliance with the DDBJ/ENA/GenBank
consortium's rules and international standards.
3. Accession Number Assignment and
Notification: The INSDC will allocate a unique
number to a Contact Person whose e-mail
address is entered in the field “Contact
person”. Normally, this notice is sent within five
working days.

22.  4. Notification of Data Release:
DDBJ data are accessible through getentry and
anonymous FTP. The data are transmitted to
GenBank and ENA, and are also accessible via
GenBank and ENA. The data also include DDBJ,
Search and Analysis services and ARSA
services. Essentially, the data published by
DDBJ are open to the public.

23.  National Center for Biotechnology (https://www.ncbi.nlm.nih.gov)
 It is part of National Library of Medicine (NLM), a branch of National
Institute of Health (NIH).
 NCBI (National Center For Biotechnology Information) is widely used
Database for nucleotide, gene and protein.
 Established in 1988.
 Aim: To create a public data base, develop software tool such as
Sequence analysis, Biomedical information, mainly to aid the
research in computational biology protein sequence retrieval.

24.  Very comprehensive biological database
 GENBANK: The nucleotide sequence database
 Provides 42 different resource
 Provides a simple and easy to use web interface
http://www.ncbi.nlm.nih.gov/
 Sequence submission: done using Bankit or
Sequin
 Search Engine for data retrieval: Entrez: Retrieves
information across all the resources under NCBI
Example:
 PubMed, taxonomy, SNP, PubChem etc.

26.  The NCBI database contains several sub-
databases, the most important of which are:
 1. NCBI Nucleotide database: contains DNA and
RNA sequences
 2. NCBI Protein database: contains protein
sequences
 3. EST: contains ESTs (expressed sequence tags),
which are short sequences derived from mRNAs
 4. The NCBI Genome database: contains DNA
sequences for whole genomes
 5. PubMed: contains data on scientific
publications

27.  It also contain some tools
a. Database retrieval tool
e.g Entrez : for data retrieval
b. Specialized tool E.g. BLAST tool to know
about classification and function of any known
nucleotide sequence

28. Entrez
Web address:
http//www.ncbi.nlm.nih.gov/Entrez
 It is a molecular database retrieval system
developed by NCBI.
 Easy to use, and is highly convenient, user don’t
have to visit multiple database, as it displays all the
links of information in single page.
 It allows text-based search for a wide variety of
data.

29.  For each sequence the NCBI database stores some extra
information such as the species that it came from,
publications describing the sequence, etc. This
information is stored in the NCBI entry or NCBI record for
the sequence.
 The NCBI entry for a sequence can be viewed by searching
the NCBI database for the accession number for that
sequence.
 The NCBI entries for sequences are stored in a particular
format, known as NCBI format.
 To view the NCBI entry for the DEN-1 Dengue virus (which
has accession NC_001477), follow these steps:
 1. Go to the NCBI website (www.ncbi.nlm.nih.gov).
 2. Search for the accession number.

30. On the results page, if your sequence corresponds to a
nucleotide (DNA or RNA) sequence, you should see a
hit in
the Nucleotide database, and you should click on the
word ‘Nucleotide’ to view the NCBI entry for the hit.
4. Likewise, if your sequence corresponds to a protein
sequence, you should see a hit in the Protein database,
and you should click on the word ‘Protein’ to view the
NCBI entry for the hit.
5. After you click on ‘Nucleotide’ or ‘Protein’ in the
previous step, the NCBI entry for the accession will
appear.

32. The NCBI entry for an accession contains a lot of information
about the sequence ,such as:
1. The ‘LOCUS’ field gives the information about length,
accession number and when it was reported.
2. The ‘DEFINITION’ field gives a short description for the
sequence.
3. The ‘ORGANISM’ field in the NCBI entry identifies the
species that the sequence came from.
4. The ‘REFERENCE’ field contains scientific publications
describing the sequence.
5. The ‘FEATURES’ field contains information about the
location of features of interest inside the sequence, such as
regulatory sequences or genes that lie inside the sequence.
6. The ‘ORIGIN’ field gives the sequence itself.

34.  Sequence Submission Tools:
 If we want to submit a new genomic sequence to
NCBI, then we can use tools like Bankit and
Sequin.
1. Bankit• Web-based sequence submission tool•
Present on NCBI Homepage Tool for Simple
submission: when only one or small number of
records are to be submitted.
Can also be used by submitters to update their
existing GenBank.

35. 2. Sequin
 NCBI tool for sequence submission and
update.
 Can handle multiple sequence submissions;
that includes long sequences, multiple
annotations, segment sets of DNA,
population studies
 Provide graphical viewing and editing options

37.  Open NCBI.
 Choose ‘’gene’’ in all databases option

40. Position of
gene
Exons Introns

41.  Open NCBI on your browser
 Select option “nucleotide” and press
enter
 Search for any gene

43. Date of
submission
Keywords

44.  Open NCBI
 From ‘’all database’’ choose genome
 Type the name of organism e.g. Human
genome

46.  The European Molecular Biology Laboratory (EMBL) is
a molecular biology research institution supported
by 20 European countries and Australia as associate
member state.
 EMBL was created in 1974 and is an intergovernmental
organization funded by public research money from its member
states.
 Research at EMBL is conducted by approximately 85
independent groups covering the spectrum of molecular
biology.
 The Laboratory operates from five sites: the main Laboratory in
Heidelberg, and Outstations in Hinxton (the European
Bioinformatics Institute (EBI)), Grenoble, Hamburg, and
Monterotondo near Rome.

47. The cornerstones of EMBL's mission are:
 to perform basic research in molecular biology; to train scientists,
students and visitors at all levels.
 Basic research in molecular biology and molecular medicine is
performed; scientists, students and visitors at all levels are
trained; vital services to scientists in the member states are
offered.
 New instruments and methods in the life sciences are developed;
and there is an active engagement in technology transfer.
 Many scientific breakthroughs have been made at EMBL, most
notably the first systematic genetic analysis of embryonic
development in the fruit fly by Christiane Nüsslein-Volhard and
Eric Wieschaus, for which they were awarded the Nobel Prize for
Medicine in 1995

48.  Advanced training is one of EMBL's core missions.
 Over the years, the Laboratory has established a
number of training activities, of which the EMBL
International PhD Programme (EIPP) is the flagship - it
has a student body of about 200, and since 1997 has
had the right to award its own degree.
 Other activities include the postdoctoral programme,
including the EMBL Interdisciplinary Postdoctoral
programme (EIPOD); the European Learning
Laboratory for the Life Sciences (ELLS) for teacher
training; and the Visitor Programme.

49. EMBL-Bank (www.ebi.ac.uk/embl/), which
began its life as the EMBL Data Library at
the European Molecular Biology
Laboratory's Heidelberg headquarters in
1980, was the world's first publicly
available database of nucleotide
sequence.

50.  The European Bioinformatics Institute (EBI) is
a centre for research and services in
bioinformatics, and is part of European
Molecular Biology Laboratory(EMBL)
 EMBL-EBI grew out of EMBL'S pioneering work
to provide public biological database to
research community.

51.  The European Bioinformatics Institute (EBI) is part of the
European Molecular Biology Laboratory (EMBL) and is
located on the Wellcome Trust Genome Campus in Hinxton
near Cambridge (UK).
 The EBI grew out of EMBL's pioneering work in providing
public biological databases to the research community.
 It hosts some of the world's most important collections of
biological data, including DNA sequences (EMBL-Bank),
protein sequences (UniProt), animal genomes (Ensembl),
three-dimensional structures (the Macromolecular
Structure Database).The EBI hosts several research groups
and its scientists continually develop new tools for the
biocomputing community

52.  In 1980, the EMBL Nucleotide Sequence Data
Library (now part of the European Nucleotide
Archive) was established in EMBL Heidelberg,
with the goal of creating a central database of
DNA sequences.
 In 1992, the EMBL Council voted to establish
EMBL’s European Bioinformatics Institute (EMBL-
EBI) on the Wellcome Genome Campus in
Hinxton, UK, where it would be in close
proximity to the major sequencing efforts at the
Wellcome Sanger Institute.
 The transition of two major bioinformatics
services from Heidelberg to Hinxton began in
1992 and in September 1994, EMBL-EBI was
firmly established in the UK.

54.  To built, maintain, and prepare biological
databases and make them available to the
scientific community.

55. Data at EMBL-EBI spans
genomics, proteins,
expression, small molecules,
protein structures, systems,
ontologies and scientific
literature.

56.  EMBL-EBI gathers biological information from both
published literature and directly from experimental
research.
 This data is then processed, incorporated into all
relevant databases, classified, annotated, and aligned
with existing data to become a value-added
resources.
 These resources are provided as defined services.
The most strategically important databases are
accompanied by comprehensive tools and training.
 This allows scientists to share data, perform complex
queries, and analyze results in different ways.
Scientists can work locally by downloading EMBL-EBI
data and software or use web services to access
EMBL-EBI resources programmatically

57.  The main activity of the group is the development,
maintenance and distribution of a comprehensive
database of nucleotide sequences.
 The EMBL nucleotide sequence database, produced in
collaboration with GenBank and the DNA database of
Japan, is Europe's primary nucleotide sequence data
resource.
 Each of these three groups collect a portion of the
total sequence data reported world-wide. All new and
updated database entries are exchanged between the
groups on a daily basis.

60.  Results 0f ‘’EMBL’’  Results of FASTA