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    Introduction To NCBI

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    Introduction To NCBI

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    Introduction to NCBI

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    Introduction To NCBI

    Uploaded by

    zari_pak2010

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    © All Rights Reserved
    Download as PDF, TXT or read online from Scribd
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    of 31

    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
    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

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