Scribd
Upload
45 views29 pages

Introduction To NCBI

Uploaded by

Furqan Ahmad Khan
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as PPTX, PDF, TXT or read online on Scribd
45 views29 pages

Introduction To NCBI

Uploaded by

Furqan Ahmad Khan
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as PPTX, PDF, TXT or read online on Scribd
You are on page 1/ 29

Introduction to NCBI

By
Dr Anwar Ullah
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
(
http://www.ncbi.nlm.nih.
gov/
)
Overvi
ew

All
Databases Popular
RAelsloDuracteasbases
a
nd Tools
Cli
ck
"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.
Clic
k Cli
ck
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 3: Click Triticum
Step 2: Click Plants 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

You might also like