INTRODUCTION OF BIOINFORMATICS HISTORY WHAT IS DATABASE NEED FOR DATABASE TYPES OF DATABASE PRIMARY DATABASE NUCLEIC ACID SEQUENCE DATABASE GENE BANK INTRODUCTION GENE BANK SUBMISSION TOOL GENE BANK SUBMISSION TYPE HOW TO RETRIEVE DATA FROM GENEBANK APPLICATION CONCLUSION REFERENCE

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GENBANK
By
KAUSHAL KUMAR SAHU
Assistant Professor (Ad Hoc)
Department of Biotechnology
Govt. Digvijay Autonomous P. G. College
Raj-Nandgaon ( C. G. )

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SYNOPSIS
INTRODUCTION OF BIOINFORMATICS
HISTORY
WHAT IS DATABASE
NEED FOR DATABASE
TYPES OF DATABASE
PRIMARY DATABASE
NUCLEIC ACID SEQUENCE DATABASE
GEN BANK 02

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GEN BANK 03
GENE BANK
INTRODUCTION
GENE BANK SUBMISSION TOOL
GENE BANK SUBMISSION TYPE
HOW TO RETRIEVE DATA FROM GENEBANK
APPLICATION
CONCLUSION
REFERENCE

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INTRODUCTION OF BIOINFORMATICS
According to old concept BI is the symbiotic
relationship between computational and biological
science which was originally coined for the analysis
and management of biological information stored in
databases.
According to the new concept bioinformatics can be
considered as information technology applied to the
management and analysis of biological data.

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WHAT IS DATABASE
The collection of a biological data on a computer
which can be manipulated to appear in varying
arrangement and subsets is regarded as database.
Biological database are computer sites that organize,
store and disseminate files that contain information
consisting of literature references, nucleic acid
sequences, protein sequence & protein structure.

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NEED FOR DATABASE
Easy access to the information.
Method for extracting specific/required
data.
Gene discovery.
Gene function.
Protein function.
Drug discovery.
Drug designing.

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TYPES OF DATABASE
Primary database
Composite database
Secondary database

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PRIMARY SEQUENCE DATABASE
A primary database is a database that stores biomolecular
sequence (protein or nucleic acid) associated annotation
information (organism, species, functions ,mutation linked to
particular disease, functional/structural patterns.)

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NUCLEIC ACID DATABASE
DNA and protein are complicated 3D molecules,
composed of thousands or even millions of atoms bonded
together. DNA and proteins are both polymers, chains of
repeating chemical units with a common backbone holding
together.
In DNA four nucleic acid monomers (A,T,C and G) are
commonly used to build the polymer chain, the four nucleic
acids can occur in any order, and the order they occur
determines what the DNA does.

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THERE ARE THREE PRINCIPLE TYPES OF
DATABASE
GENBANK
EMBL (Europe)
DNA Data Bank Japan (DDBJ)

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Genebank EMBL
(USA) (Europe)
DDBJ
Three Principle DNA
Sequence Database

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GenBank is the DNA database from the National Centre
for Biotechnology Information (NCBI). NCBI is a division
of National Library of Medicine, located at National
Institute of health (NIH) in Bethesda in Maryland
.
It incorporates sequences from publicly available sources
,primary from direct author submission and large scale
sequencing projects.
GenBank

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NCBI maintain sequence maintain from every organism,
every source, every type of DNA from mRNA to cDNA to
clone to expressed sequence tags (ETSs) to high throughput
genome sequencing data and information about sequence
polymorphisms.
There are approximately 126,551,501,141 bases in
135,440,924 sequence records in the traditional GenBank
divisions and 191,401,393,188 bases in 62,715,288 sequence
records in the division of April 2011.
Reference-www.ncbi.nlm.nih.gov/genbank/

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GenBank Search : Main Sequence Types
GENBANK 14

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PRI
ROD
MAM
VRT
INV
PLA
BCT
RNA
VRL
Primate
Rodent
Mammalian
Vertebrate
Invertebrate
Plant, Fungal
Bacterial
Structural
RNA
Viral
PHG
SYN
EST
PAT
STS
GSS
Bacteriophage
Synthetic
Expressed Sequence Tags
Patent
Sequence tagged sites
Genome Survey Sequence
The increasing size of the database and the diversity of data sources
available have made it convenient to split Genebank into smaller
discrete division.

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GENBANK SUBMISSION TYPE
GenBank accepts mRNA or genomic sequence data directly
determined by the submitter.
The submission must include information about the source
organism and annotation provided by the submitter.
More details about adding annotation and sample files can
be found in the GenBank Submissions Handbook

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The following data is not accepted by GenBank
Primer sequences
Protein sequences with no underlying
nucleotide submission
Sequence containing a mix of genomic and
mRNA sequence
Sequences with length less than 200
nucleotides
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HOW TO SUBMIT DATA TO GENBANK
The most important source of new data for GenBank is
direct submissions from scientists. GenBank depends on
its contributors to help keep the database as
comprehensive, current, and accurate as possible.
NCBI provides timely and accurate processing and
biological review of new entries and updates to existing
entries, and is ready to assist authors who have new data
to submit.

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Receiving an Accession Number for your Manuscript
Most journals require DNA and amino acid sequences that
are cited in articles be submitted to a public sequence
repository (DDBJ/EMBL/Genbank) as part of the publication
process.
Data exchange between DDBJ, EMBL and GenBank
occurs daily so it is only necessary to submit the sequence to
one database, whichever one is most convenient, without
regard for where the sequence may be published.

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Updating or Revising a GenBank Sequence
Revisions or updates to GenBank entries can be
made by the submitters at any time.
Information about the correct format for different
types of updates can be found on the Update
guidelines page.

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Confidentiality
Some authors are concerned that the appearance of their
data in GenBank prior to publication will compromise their
work. GenBank will, upon request, withhold release of new
submissions for a specified period of time.
However, if a paper citing the sequence or accession
number is published prior to the specified date, your
sequence will be released upon publication.

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Privacy
If you are submitting human sequences to GenBank, do not
include any data that could reveal the personal identity of the
source. It is our assumption that you have received any
necessary informed consent authorizations that your
organizations require prior to submitting your sequences.

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HOW TO RETRIEVE DATA FROM GENBANK
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APPLICATIONS OF GENBANK
SEQUENCE ALIGNMENTS
PRIMER DESIGNING
GENE EXPRESSION AND DNA MICROARRAY
IN CROP IMPROVEMENT
IN EVOLUTION
.

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References
1.Bioinformatics :C.S.V.Murthy
2.BIOINFORMATICS : David W.Mount
3.By Internets
www.ncbi.nlm.nih.gov/genbank/
www.ncbi.nlm.nih.gov › NCBI› DNA & RNA