Introduction to NCBI

From:
Geetika Jethra
Senior Research Fellow
Unit of Simulation and Informatics
Indian Agricultural R...
NCBI

National Centre for Biotechnology Information
(http://www.ncbi.nlm.nih.gov/)
Established

as the government's respo...
NCBI along with EBI and CIB together
form International Sequence Database
Collaboration which act as the chief
working uni...
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

"

Databases and Tools" from the yields a

definitions and introductory i...
Entrez : A retrieval system
Capable of accessing integrated
information by searching many of the
NCBI databases with just ...
Entrez: Home Page
Entrez – Home Page
BLAST
Basic Local Alignment Search Tool
A predominant sequence alignment tool
for performing rapid searches of
nucleotide ...
Exercise 1: To search nucleotide sequence
data of Oryza sativa and download the data
into a separate text file in
(i) GenB...
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 th...
Exercise 4: To view the graphics file of
Chain A, Solution Structure of Plant
Nsltp2 Purified from Rice (Oryza Sativa)
and...
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 ...
Step 4: Result by MMDB
Introduction to NCBI
Introduction to NCBI
Introduction to NCBI
Introduction to NCBI
Introduction to NCBI
Introduction to NCBI
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Introduction to NCBI

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This presentation will tells about the Introduction and working of NCBI database and is informative for the beginners.

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Introduction to NCBI

  1. 1. Introduction to NCBI From: Geetika Jethra Senior Research Fellow Unit of Simulation and Informatics Indian Agricultural Research Institute
  2. 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. 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. 4. International Sequence Database Collaboration Working
  5. 5. NCBI - Home Page (http://www.ncbi.nlm.nih.gov/)
  6. 6. Overview All Databases Popular Resources All Databases and Tools
  7. 7. Click
  8. 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. 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. 10. Entrez: Home Page
  11. 11. Entrez – Home Page
  12. 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. 13. 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.
  14. 14. Oryza Sativa Click
  15. 15. Click Click
  16. 16. Exercise 2: To View the Genome Map of Oryza sativa with chromosome number.
  17. 17. Exercise 3:Download the sequence data i.e. contigs from the ftp site of NCBI.
  18. 18. Step 1: Open NCBI Home page -> FTP site -> Genome assembly/Annotation Projects
  19. 19. Step 2: Click Plants Step 3: Click Triticum aestivum
  20. 20. 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
  21. 21. 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.
  22. 22. Step 1: NCBI Home Page -> Proteins -> click on the first link
  23. 23. Step 2: 1st Result
  24. 24. 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.
  25. 25. Step 4: Result by MMDB
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