Module 3: DNA Databases and Sequence Queries

 

Exercise 3

Sequence search and retrieval methods module 3 contents back to the index of modules


  • We will search (query) for a DNA and a protein sequence using the Entrez search engine.

    DNA Sequence Search

    1. Go to the Entrez site and click on the "Nucleotide" icon.
    2. Search for "Murine T cell receptor gamma chain" (no quotes needed).
    3. Choose the item #1 (Accession # X65622) for the promoter region of the gamma-4 gene and select the "GenBank" option from the Display menu.
      Notice that the search produced a DNA sequence for the promoter and a variety of other data about this sequence, such as the Medline article reference (PUBMED) for it, salient features within it etc.,
    4. The Display menu can also be used for locating a corresponding protein sequence. In this case, there is no such sequence since the DNA sequence is for a regulatory element (promoter) although, the translational start codon ATG is present at the 3' end (# 552-554).
    5. Familiarize yourself with other available options for each nucleotide sequence shown.

    Protein Sequence Search

    1. Go to the Entrez site as above and click on the "Protein" icon.
    2. Search for "Murine interleukin 7 receptor alpha chain" (no quotes needed). Also, before you click the "Go" button, note that you can retrieve 3-D structures of a protein from the Entrez structure database.
    3. Choose the item # 2 (Accession # AAF06717) by selecting the "GenPept" option on the Display menu for the whole polypeptide sequence.
      Notice that the sequence of the murine interleukin 7 receptor alpha chain is displayed along with the publication source and details regarding the polypeptide.
    4. From the sequence display screen, one can display the graphics of how the sequence is laid out. This is an useful graphical tool for publication. (Figure of IL-7R sequence)
    5. Familiarize yourself with other available options for each protein sequence shown.

  • There are a number of useful, common tools which can be employed during DNA or protein searches.
    1. As noted above, the graphics tool can be used for publication-ready figures. This tool is more relevant for genomic sequence to show exons and introns. (Pick a genomic sequence of your interest and try the graphics tool on it; or try it during a nucleotide search for "human p53 tumor suppressor" and pick one of the sequences with exons and introns, eg., AF210309 or AF210310)
    2. Sequences can be viewed in the FASTA format for copying and pasting to a similarity search or alignment (see Module 4 and Module 5).
    3. You can save the searches or put them on the Clipboard for word processing tasks. (Try copying the DNA sequence of the promoter region of the TCR gamma chain on to your computer using a word processing program such as "Notepad".)
    4. One can search for a variety of links such as protein, nucleotide neighbor, genome, structure etc., that are related to the query sequence.


Sequence search and retrieval methods module 3 contents back to the index of modules

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