database of nucleic acid

1. PRIMARY SEQUENCE
DATABASE OF NUCLEIC ACID
Presented by: Vibha (Pharmaceutics)

2. DEFINITION
•It consist of experimentally derived data such as
nucleotide, protein sequence, or macromolecular
structure.
•Experimental results are submitted directly into
database by researchers.
•The nucleic acid sequence databases contain
sequences of DNA and/or RNA sequences.
• The databases EMBL, GenBank and DDBJ are
three primary DNA sequence databases.

3.  There is comparatively little error checking and there is a fair amount
of redundancy
 The entries in the EMBL, GenBank and DDBJ databases are
synchronized on a daily basis, and the accession numbers are
managed in a consistent manner between these three centers.
 The nucleotide databases have reached such large sizes that they are
available in subdivisions that allow searches or downloads that are
more limited, and hence less time-consuming.
 There are no legal restrictions on the use of the data in these
databases. However, there are patented sequences in the databases.

4. GENBANK OR NCBI
 It offers a daily exchange of information with other
major sequence databases, has a variety of user
interfaces, fairly detailed online help (with e-mail
addresses for more information if what is already
available is not sufficient), and a speedy interface.
 Established by the National Center for Biotechnology
Information (NCBI) 1988 in, GenBank is a collection of
all known DNA sequences from scientists around the
world.

5.  BANKIT is a web based Genbank sequence submission tool.
This is required for submitter to connect to NCBI home page
and select the Genbank link from lift side bar.
 Sequin is a software tool developed by NCBI which helps in
submission and updating entries to sequence database and help
in handling multiple sequence submission.
 Submitting sequences to Gen Bank is also very easy and is
required by most journals before articles pertaining to the
sequence are published (this provides easy access to the
information for the journal's readers).
 Also provide graphical description.
 Entry include concise description of the sequence, scientific
name of source organism, and table of features testing
biologically significant like coding regions.
 Accession number, version etc.

6. EMBL
EUROPEAN MOLECULAR BIOLOGY LABORATORY
 It was created in 1974.
 EMBL is good to use when you need a limited amount of data and
when you are not trying to identify a gene by sequence analysis.
 All the servers of EMBL are situated in Europe, searching and
accessing the database may be slow.
 It part of INSDC (International Nucleotide Sequence Database
Collaboration) which includes DDBJ and GenBank.
 Aim to build, maintain and prepared biological database and the
computational services to support data deposition and data analysis
and make them available to scientific community.
 FTP sever stand for file transfer protocol which is standard network
protocol used to transfer files from one host to another host.

7.  All of the information submitted to EMBL is mirrored daily in both
GenBank and DDBJ, so searching elsewhere might provide the same
amount of information in less time.
 Database release are produced quarterly and integrated into the EBI ,
SRS (Sequence Retrieval System).
 SRS is integrated and links comprehensive collection of specialized
databank with main nucleotide database.
 CLUSTALW , PRATT etc are some analysis tool provided in EMBL.
 EMBL flat files comprises a series of controlle line presented in a
tabular manner, consist of four major blocks of data : description ,
citation, feature and sequence.
 EMBL sequences are stored in a form corresponding to the
biological state of the information in vivo.
 Thus, cDNA sequences are stored in the database as RNA sequences,
even though they usually appear in the literature as DNA.

8. DDBJ
DNA DATABANK OF JAPAN
 DDBJ, the DNA Data Bank of Japan, was established in
1986 to be one of the major international DNA
Databases (with GenBank and EMBL).
 It is certified to collect information from researchers and
assign accession numbers to submitted entries.
 It is a primary biological database that accepts DNA
sequences.
 It is located in National Institute of Genetics (NIG) in
Shizuoka Prefecture of Japan.
 It is funded by Japanese Ministry of Education, Culture,
sports, science and technology.