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 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. 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.
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
