Gene bank by kk sahu

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 01
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
AccordingtooldconceptBIisthesymbiotic
relationshipbetweencomputationalandbiological
sciencewhichwasoriginallycoinedfortheanalysis
andmanagementofbiologicalinformationstoredin
databases.
Accordingtothenewconceptbioinformaticscanbe
consideredasinformationtechnologyappliedtothe
managementandanalysisofbiologicaldata.

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WHAT IS DATABASE
Thecollectionofabiologicaldataonacomputer
whichcanbemanipulatedtoappearinvarying
arrangementandsubsetsisregardedasdatabase.
Biologicaldatabasearecomputersitesthatorganize,
storeanddisseminatefilesthatcontaininformation
consistingofliteraturereferences,nucleicacid
sequences,proteinsequence&proteinstructure.

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NEED FOR DATABASE
Easyaccesstotheinformation.
Methodforextractingspecific/required
data.
Genediscovery.
Genefunction.
Proteinfunction.
Drugdiscovery.
Drugdesigning.

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TYPES OF DATABASE
Primarydatabase
Compositedatabase
Secondarydatabase

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PRIMARY SEQUENCE DATABASE
Aprimarydatabaseisadatabasethatstoresbiomolecular
sequence(proteinornucleicacid)associatedannotation
information(organism,species,functions,mutationlinkedto
particulardisease,functional/structuralpatterns.)

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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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GENBANK 11
Genebank EMBL
(USA) (Europe)
DDBJ
Three Principle DNA
Sequence Database

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GenBankistheDNAdatabasefromtheNationalCentre
forBiotechnologyInformation(NCBI).NCBIisadivision
ofNationalLibraryofMedicine,locatedatNational
Instituteofhealth(NIH)inBethesdainMaryland
.
Itincorporatessequencesfrompubliclyavailablesources
,primaryfromdirectauthorsubmissionandlargescale
sequencingprojects.
GenBank

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NCBImaintainsequencemaintainfromeveryorganism,
everysource,everytypeofDNAfrommRNAtocDNAto
clonetoexpressedsequencetags(ETSs)tohighthroughput
genomesequencingdataandinformationaboutsequence
polymorphisms.
Thereareapproximately126,551,501,141basesin
135,440,924sequencerecordsinthetraditionalGenBank
divisionsand191,401,393,188basesin62,715,288sequence
recordsinthedivisionofApril2011.
Reference-www.ncbi.nlm.nih.gov/genbank/

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GenBankSearch : 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
Theincreasingsizeofthedatabaseandthediversityofdatasources
availablehavemadeitconvenienttosplitGenebankintosmaller
discretedivision.

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GENBANK SUBMISSION TYPE
GenBankacceptsmRNAorgenomicsequencedatadirectly
determinedbythesubmitter.
Thesubmissionmustincludeinformationaboutthesource
organismandannotationprovidedbythesubmitter.
Moredetailsaboutaddingannotationandsamplefilescan
befoundintheGenBankSubmissionsHandbook

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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
ThemostimportantsourceofnewdataforGenBankis
directsubmissionsfromscientists.GenBankdependson
itscontributorstohelpkeepthedatabaseas
comprehensive,current,andaccurateaspossible.
NCBIprovidestimelyandaccurateprocessingand
biologicalreviewofnewentriesandupdatestoexisting
entries,andisreadytoassistauthorswhohavenewdata
tosubmit.

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ReceivinganAccessionNumberforyourManuscript
MostjournalsrequireDNAandaminoacidsequencesthat
arecitedinarticlesbesubmittedtoapublicsequence
repository(DDBJ/EMBL/Genbank)aspartofthepublication
process.
DataexchangebetweenDDBJ,EMBLandGenBank
occursdailysoitisonlynecessarytosubmitthesequenceto
onedatabase,whicheveroneismostconvenient,without
regardforwherethesequencemaybepublished.

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Updating or Revising a GenBank Sequence
RevisionsorupdatestoGenBankentriescanbe
madebythesubmittersatanytime.
Informationaboutthecorrectformatfordifferent
typesofupdatescanbefoundontheUpdate
guidelinespage.

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Confidentiality
Someauthorsareconcernedthattheappearanceoftheir
datainGenBankpriortopublicationwillcompromisetheir
work.GenBankwill,uponrequest,withholdreleaseofnew
submissionsforaspecifiedperiodoftime.
However,ifapapercitingthesequenceoraccession
numberispublishedpriortothespecifieddate,your
sequencewillbereleaseduponpublication.

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Privacy
IfyouaresubmittinghumansequencestoGenBank,donot
includeanydatathatcouldrevealthepersonalidentityofthe
source.Itisourassumptionthatyouhavereceivedany
necessaryinformedconsentauthorizationsthatyour
organizationsrequirepriortosubmittingyoursequences.

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HOW TO RETRIEVE DATA FROM GENBANK
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APPLICATIONS OF GENBANK
SEQUENCEALIGNMENTS
PRIMERDESIGNING
GENEEXPRESSIONANDDNAMICROARRAY
INCROPIMPROVEMENT
INEVOLUTION
.

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