The National Center for Biotechnology Information (NCBI) was established in 1988 to develop public databases and software tools for spreading biomedical information. It maintains various biological databases such as GenBank and provides the Entrez retrieval system for accessing DNA and protein sequence data. NCBI also offers tools for sequence submission and analysis, including BankIt for simple submissions and Sequin for handling multiple sequences.

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
5nstitutes of Health, Bethesda, Maryland, USA.

3. Aim of NCBI
Develop
Public Databases
Software Tools Spread Biomedical
Information

4. 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. e.g. Entrez
3. Provide computational resources for the analysis of GenBank data.

5. NCBI Database & Resources

6. DATABASE RETRIEVAL SYSTEM
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.

7. NCBI
Link
Cross-references
Sequence
Abstract of
Paper
Protein
sequence
Coding DNA
Sequence
Protein
Sequence
3D structures

8. Architecture of Entrez

9. Sequence Submission to NCBI
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. Sequence Submission to NCBI
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 seectable
minimum size.
ORF Finder
Detection of ORF
In User’s sequence In a sequence already in
the database

12. Specialized tools
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. Specialized tools
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.