The document provides an introduction to the National Center for Biotechnology Information (NCBI), highlighting its role in managing large biological data and offering multiple databases, such as GenBank and EMBL. It describes features like the Entrez retrieval system, various bioinformatics tools including BLAST, and practical exercises for searching and downloading genomic data on Oryza sativa. Overall, it serves as a primer for using NCBI's resources effectively in bioinformatics research.

1. Introduction to NCBI
From:
Geetika Jethra
Senior Research Fellow
Unit of Simulation and Informatics
Indian Agricultural Research Institute

2. NCBI
National Centre for Biotechnology Information
(http://www.ncbi.nlm.nih.gov/)
Established
as the government's response to the
need for more and better information processing
methods to deal with vast amount of data.
Developed by National Library of Medicine (NLM)
at the National Institutes of Health (NIH)
A comprehensive website for biologists including:
biology-related
databases,
tools for viewing and analyzing
automated systems for storing and retrieval

3. NCBI along with EBI and CIB together
form International Sequence Database
Collaboration which act as the chief
working unit and Information Centre. NCBI
has 3 collaborative databases:
GenBank
European Molecular Biology Laboratory
(EMBL) Database
DNA Database of Japan (DDBJ)

4. International Sequence Database Collaboration
Working

5. NCBI - Home Page
(http://www.ncbi.nlm.nih.gov/)

6. Overview
All Databases
Popular Resources
All Databases
and Tools

7. Click

8. "
A Science Primer" yields access to general
"
Databases and Tools" from the yields a
definitions and introductory information
regarding the branches of science
included in bioinformatics.
Many bioinformatics terms are defined in
this section in a clear-cut and basic
manner, making this Primer an excellent
first resource.
complete and well-ordered listing of
accessible information.

9. Entrez : A retrieval system
Capable of accessing integrated
information by searching many of the
NCBI databases with just one query
NOTE: instead of searching only one
database per query, then repeating
the same query to find information on
the same topic from another NCBI
database).

10. Entrez: Home Page

11. Entrez – Home Page

12. BLAST
Basic Local Alignment Search Tool
A predominant sequence alignment tool
for performing rapid searches of
nucleotide and protein sequence
databases
Detecting local, as well as
global, sequence alignments between
the query and database sequences.

15. Exercise 1: To search nucleotide sequence
data of Oryza sativa and download the data
into a separate text file in
(i) GenBank format
(ii) FASTA format.

16. Oryza Sativa
Click

18. Click
Click

19. Exercise 2: To View the Genome Map
of Oryza sativa with chromosome
number.

22. Exercise 3:Download the sequence
data i.e. contigs from the ftp site of
NCBI.

23. Step 1: Open NCBI Home page -> FTP site -> Genome
assembly/Annotation Projects

24. Step 2: Click Plants
Step 3: Click Triticum aestivum

25. Step 4: Click on the link -> Save
NOTE: The file in the form of Zip format will be saved in the desired
location or in the default folder i.e. C: Downloads

26. Exercise 4: To view the graphics file of
Chain A, Solution Structure of Plant
Nsltp2 Purified from Rice (Oryza Sativa)
and the structure of Starch Branching
Enzyme I (Bei) From Oryza Sativa L.

27. Step 1: NCBI Home Page -> Proteins -> click on the first link

28. Step 2: 1st Result

29. Step 3: Go to home page of Entrez -> click on the 2nd link
1
2
3
4
5
1
Click to download the PDB file and view the structure using Cn3D software.
2
To view the PubMed i.e. to open the research articles and abstracts.
3
To view the protein files associated with Starch Branching Enzyme I (Bei) from Oryza Sativa L.
4
To view the conserved domain associated with the link.
5
To view the chemical structure of the protein along with the molecular weight and chemical formula for t
the same.

30. Step 4: Result by MMDB