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Introduction To NCBI

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Introduction to NCBI

From:
Geetika Jethra
Senior Research Fellow
Unit of Simulation and Informatics
Indian Agricultural Research Institute
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
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)
International Sequence Database Collaboration
Working
NCBI - Home Page
(http://www.ncbi.nlm.nih.gov/)
Overview

All Databases
Popular Resources
All Databases
and Tools
Click
" A Science Primer" yields access to general
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.

" Databases and Tools" from the yields a


complete and well-ordered listing of
accessible information.
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).
Entrez: Home Page
Entrez – Home Page
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.
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.
Oryza Sativa

Click
Click Click
Exercise 2: To View the Genome Map
of Oryza sativa with chromosome
number.
Exercise 3:Download the sequence
data i.e. contigs from the ftp site of
NCBI.
Step 1: Open NCBI Home page -> FTP site -> Genome
assembly/Annotation Projects
Step 2: Click Plants Step 3: Click Triticum aestivum
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\
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.
Step 1: NCBI Home Page -> Proteins -> click on the first link
Step 2: 1st Result
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.


To view the chemical structure of the protein along with the molecular weight and chemical formula for t
5 the same.
Step 4: Result by MMDB

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