NCBI National Center for Biotechnology Information

The National Center for Biotechnology Information advances science and health by providing access to biomedical and genomic information

1. National Center for
Biotechnology Information
NCBI
Amandeep Singh
Assistant Professor
Department of Biotechnology
GSSDGS KhalsaCollege Patiala

2. Introduction
National Library of Medicine
NCBI
National Institute of Health, Bethesda, Maryland, USA
NCBIisestablishedin1988asapartofNationalLibraryofMedicineatthe
NationalInstitutesofHealth,Bethesda,Maryland,USA.

3. •TheNCBIhousesaseriesofdatabasesrelevantto
biotechnologyandbiomedicineandconsistsofimportant
resourcesforbioinformaticstoolsandservices.
•MajordatabasesincludeGenBankforDNAsequencesand
PubMed,abibliographicdatabaseforbiomedicalliterature.
•MajorResourcesincludesBooks,softwaretools(BLAST),
retrievalsystem(Entrez),submissiontools(Bankit,Sequin),
specializedtools(ORFFinder,e-PCR,Spidey/Splign).

4. Aim of NCBI
1. To Develop
Public Databases
2. To Develop Software Tools 3. To Spread
Biomedical
Information

5. Roles of NCBI
1. Maintenance of Biological Databases. e.g. GenBank
Primary Secondary/Derivative
1. Original submissionby experimentalists.1. Built up from primary database
2. Contentcontrolled by submitter. 2. Content controlled by third body (NCBI)
2. Provide data retrieval system (if we want to retrieve the data form
biological databases, we need retrieval system). e.g. Entrez
3. Provide computational resources for the analysis of GenBankdata.
(only after analysis we can use the information available in databases,
so we need computational resources)

6. NCBI Database & Resources

7. DATABASE RETRIEVAL SYSTEM-
Entrez
Entrez:Integrateddatabasesearchandretrievalsystem.
•ExtractinformationfromDNAsequencedata,protein
sequencedata,populationset,wholegenome,
macromolecularstructures,biomedicalliteraturelike
PubMed.
•Sequencesources:PIR,SWISS-PROT,PDB,
GenBank,RefSeq.
•Coversover20databases.

8. Protein Information
Protein Sequence
Protein Structure
PIR
SWISS-PROT
PDB
GenBank Genetic Sequence
RETRIEVAL SYSTEM
Name of
DATABASES
Information
Provided
Information
Accessible to the
User
Entrez

9. Sequence Submission Tools
IfwewanttosubmitanewgenomicsequencetoNCBI,thenwecanuse
toolslikeBankitandSequin.
1.Bankit
•Web-basedsequencesubmissiontool
•PresentonNCBIHomepage
•ToolforSimplesubmission:whenonlyoneorsmallnumberof
recordsaretobesubmitted.
•CanalsobeusedbysubmitterstoupdatetheirexistingGenBank
records.
•Sequenceanalysistoolsarenotrequiredforsubmissionthroughthis
process.

10. 2.Sequin
•NCBItoolforsequencesubmissionandupdate.
•Canhandlemultiplesequencesubmissions;thatincludeslong
sequences,multipleannotations,segmentsetsofDNA,
populationstudies
•Providegraphicalviewingandeditingoptions.

11. Specialized tools
1.ORFFinder
Graphicanalysistooltodetectopenreadingframe(ORF)ofaselectableminimumsize.
AnopenreadingframeisaportionofaDNAmoleculethat,whentranslatedintoamino
acids,containsnostopcodons.
ORF Finder
Detection of ORF
In User’s sequence
In a sequence already in
the database

12. 2.e-PCR
Computationprocedurethatisusedtoidentifysequence-tag-
sites(STSs)withinDNAsequence.
STSisashort(200to500basepair)DNAsequencethathasa
singleoccurrenceinthegenomeandwhoselocationandbase
sequenceareknown.
SearchforSTSsubsequencestomatchwithPCRprimerwhich
havecorrectorder,orientation,spacingtogenerateknown
STSs.

13. 3. Spidey/Splign
•mRNA to Genomic alignment program, which use the local
alignment tools-BLAST & Dot View, to find it’s alignment.
•For identification of exonsand intronsand linkbetween
them.
•For tracking splice junction.
•For identification of frameshiftsequences.
•For identification of changes in sequences.