Introduction to NCBI

Introduction to NCBI

From:Geetika JethraSenior Research Fellow Unit of Simulation and InformaticsIndian Agricultural Research Institute

NCBI

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

National Centre for Biotechnology Information

(http://www.ncbi.nlm.nih.gov/)

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:

GenBankEuropean Molecular Biology Laboratory (EMBL) DatabaseDNA Database of Japan (DDBJ)

International Sequence Database Collaboration Working

NCBI - Home Page(http://

www.ncbi.nlm.nih.gov/)

Overview

Popular Resources

All Databases

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.

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 : A retrieval system

Entrez: Home Page

Entrez – Home Page

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.

BLAST Basic Local Alignment

Search Tool

Exercise 1: To search nucleotide sequencedata 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

2 3 4 51

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Click to download the PDB file and view the structure using Cn3D software.

To view the PubMed i.e. to open the research articles and abstracts.

To view the protein files associated with Starch Branching Enzyme I (Bei) from Oryza Sativa L.

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 tthe same.

Step 4: Result by MMDB