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 Khalsa College Patiala

2. Introduction
National Library of Medicine
NCBI
National Institute of Health, Bethesda, Maryland, USA
NCBI is established in 1988 as a part of National Library of Medicine at the
National Institutes of Health, Bethesda, Maryland, USA.

3. • The NCBI houses a series of databases relevant to
biotechnology and biomedicine and consists of important
resources for bioinformatics tools and services.
• Major databases include GenBank for DNA sequences and
PubMed, a bibliographic database for biomedical literature.
• Major Resources includes Books, software tools (BLAST),
retrieval system (Entrez), submission tools (Bankit, Sequin),
specialized tools (ORF Finder, 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 submission by experimentalists. 1. Built up from primary database
2. Content controlled 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 GenBank data.
(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: Integrated database search and retrieval system.
• Extract information from DNA sequence data, protein
sequence data, population set, whole genome,
macromolecular structures, biomedical literature like
PubMed.
• Sequence sources: PIR, SWISS-PROT, PDB,
GenBank, RefSeq.
• Covers over 20 databases.

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
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
records.
• Sequence analysis tools are not required for submission through this
process.

10. 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.

11. Specialized tools
1. ORF Finder
Graphic analysis tool to detect open reading frame (ORF) of a selectable minimum size.
An open reading frame is a portion of a DNA molecule that, when translated into amino
acids, contains no stop codons.
ORF Finder
Detection of ORF
In User’s sequence In a sequence already in
the database

12. 2. e-PCR
Computation procedure that is used to identify sequence-tag-
sites (STSs) with in DNA sequence.
STS is a short (200 to 500 base pair) DNA sequence that has a
single occurrence in the genome and whose location and base
sequence are known.
Search for STS subsequences to match with PCR primer which
have correct order, orientation, spacing to generate known
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 exons and introns and link between
them.
• For tracking splice junction.
• For identification of frameshift sequences.
• For identification of changes in sequences.