Z Score,T Score, Percential Rank and Box Plot Graph
Introduction to NCBI
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)
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).
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.
13.
14.
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.
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
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.