Introduction to NCBI

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Information about Introduction to NCBI
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Published on February 21, 2014

Author: geetikaJethra

Source: slideshare.net

Description

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

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 " 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.

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. 5 To view the chemical structure of the protein along with the molecular weight and chemical formula for t the same.

Step 4: Result by MMDB

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