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    Query Sequence 8

    Uploaded by

    Nisha Lauren Vishvanath
    The document provides instructions for a student to perform a BLAST search using a 1950 nucleotide query sequence from the dataset. It asks the student 8 questions about the results of the BLAST search, instructing them to refer to BLAST tutorial materials and databases like GenBank, PubMed, Gene and UniGene to find the answers. The questions ask the student to identify information about the query sequence like its likely identity as the Rafflesia azlanii NADH dehydrogenase subunit 1 gene, the organism it came from, and the function of the protein encoded.

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    © All Rights Reserved
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    Query Sequence 8

    Uploaded by

    Nisha Lauren Vishvanath
    17 views3 pages
    The document provides instructions for a student to perform a BLAST search using a 1950 nucleotide query sequence from the dataset. It asks the student 8 questions about the results of the BLAST search, instructing them to refer to BLAST tutorial materials and databases like GenBank, PubMed, Gene and UniGene to find the answers. The questions ask the student to identify information about the query sequence like its likely identity as the Rafflesia azlanii NADH dehydrogenase subunit 1 gene, the organism it came from, and the function of the protein encoded.

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    QUERY SEQUENCE 8

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    The document provides instructions for a student to perform a BLAST search using a 1950 nucleotide query sequence from the dataset. It asks the student 8 questions about the results of the BLAST search, instructing them to refer to BLAST tutorial materials and databases like GenBank, PubMed, Gene and UniGene to find the answers. The questions ask the student to identify information about the query sequence like its likely identity as the Rafflesia azlanii NADH dehydrogenase subunit 1 gene, the organism it came from, and the function of the protein encoded.

    Copyright:

    © All Rights Reserved
    Download as DOC, PDF, TXT or read online from Scribd
    Download as doc, pdf, or txt
    17 views3 pages

    Query Sequence 8

    Uploaded by

    Nisha Lauren Vishvanath
    The document provides instructions for a student to perform a BLAST search using a 1950 nucleotide query sequence from the dataset. It asks the student 8 questions about the results of the BLAST search, instructing them to refer to BLAST tutorial materials and databases like GenBank, PubMed, Gene and UniGene to find the answers. The questions ask the student to identify information about the query sequence like its likely identity as the Rafflesia azlanii NADH dehydrogenase subunit 1 gene, the organism it came from, and the function of the protein encoded.

    Copyright:

    © All Rights Reserved
    Download as DOC, PDF, TXT or read online from Scribd
    Download as doc, pdf, or txt
    of 3

    Name : NANTHINI

    Student ID : QUERY SEQUENCE 8

    BALSTING through the kingdom of life

    Instruction:

    In short, you will copy one of the sequences from the data set, use nucleotide (blastn) in BLAST to
    identify it, and use the information from your search to answer the question below. Instructions for
    copying and pasting sequences are provided with the dataset. Instructions for using BLAST is
    provided in your tutorial.

    Materials:

     An internet connection
     Make a bookmark in your web browser to the NCBI website: http://www.ncbi.nih.gov
     A guide that shows how to do search and interpret the results is available at
    ftp://ftp.ncbi.nlm.nih.gov/pub/factsheets/HowTo_BLASTGuide.pdf
     An overview on the BLAST interface is available on
    http://blast.ncbi.nlm.nih.gov/about/#home
     A set of an "Query Sequences" (download in MyGuru) for you to identify.

    Questions: Be sure to include the source of the information along with your answer. In this case, the
    source will be the database or web page that provided the information.

    1) How long is the sequence that was used to search the database?
    Hint: This sequence is called "query" sequence because you used it to ask a question (or query)
    of the database.
    1950

    2) What is the most likely identify of this sequence? What data supports this conclusion?
    Hint: Refer to the slide in the BLAST tutorial that discuss the E-value.
    Rafflesia azlanii NADH dehydrogenase subunit 1(nad1) gene

    1 | B i o i n f o r m a ti c s T u t o r i a l S B L 1 0 3 3
    3) What organism was the most likely source of the sequence?
    Hint: Refer to the BLAST tutorial to find an overview of the GenBank nucleotide record. If more
    than one organism matches, look at the E- value to determine the most likely match.
    Rafflesia azlanii NADH dehydrogenase subunit 1(nad1) gene

    4) What is the common name for this organism?


    Hint: Refer to the GenBank nucleotide record. It may also help to look at the Taxonomy
    database. The BLAST tutorial shows where to find this link.
    Rafflesia azlanii NADH

    5) What phylum contains this organism?


    Hint: Refer to the taxonomy database. The BLAST tutorial shows how to find the link.
    Eudicots

    6) What is the accession number for the best-matching sequence?


    HM803269.1

    7) If possible, give the names of three different organisms with significant E-values. If
    organism is represented, then write down the name of that organism.
    Hint: Refer to the BLAST tutorial slide on E-value for description.
    -Rafflesia keithii NADH dehydrogenase subunit 1 (nad1) gene,
    exons 2, 3 and partial cds; mitochondrial
    -Rafflesia sp. Clemens 32422 NADH dehydrogenase subunit 1 gene,
    exons 2, 3 and partial cds; mitochondrial
    -Rafflesia kerrii NADH dehydrogenase subunit 1 (nad1) gene,
    exons 2, 3 and partial cds; mitochondrial

    2 | B i o i n f o r m a ti c s T u t o r i a l S B L 1 0 3 3
    8) Use GenBank, PubMed, Gene, and UniGene records to find the possible function of the
    protein that's specified by your DNA sequence. Describe what's known about the role of this
    protein in the organism that provided the DNA.
    Mitochondria produce energy through a process called oxidative
    phosphorylation. This process uses oxygen and simple sugars to
    create adenosine triphosphate (ATP). Mitochondrial DNA contains
    37 genes, all of which are essential for normal mitochondrial
    function.

    3 | B i o i n f o r m a ti c s T u t o r i a l S B L 1 0 3 3

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