Tutorial: Searching and Retrieving Sequence Files from GenBank

The following steps will demonstrate how to search and retrieve sequences from GenBank and have them automatically imported into GCK.

  1. To perform the following, you need to be connected to the Internet. If you are not already on line, please connect now. Choose Tools > Deluxe Import > Retrieve Sequence to start the process. You will see Figure 2.70. Enter ”J00231” (or any other accession number or sequence name you might be interested in) into the box in the top left corner. As you enter the accession number or sequence name into this box, you can see a URL being constructed in the bottom left box (this is not editable, but is shown for you to examine what GCK is actually doing for you). This URL will be sent to the server that you have designated. GenBank and EMBL are two default options, but you can also specify a local server by pressing the Set Root URL… button.
    Figure 2.70: Retrieve Sequence Dialog
  2. Pressing Retrieve will contact your target database and retrieve the sequence for you. Once the sequence is retrieved, you will see a window very much like that shown in Figure 2.67. You can proceed from that point to finish importing the sequence into GCK using the same steps described in a previous tutorial (“Cloning a DNA Segment and Silent Mutations”).
  3. You can also search GenBank using GCK. Selecting File > Deluxe Import > Search GenBank will bring up Figure 2.71, which shows the search dialog for defining how you want to search GenBank. Note that the popup menu allows you to define the database fields to be searched by your query. Type in the search expression you wish to look for and then press the Search button. A progress dialog informs you of progress, and then you will get a list of items matching your query. The list will be similar to Figure 2.68. The sequences you are interested in are now on your hard disk and can be imported directly into GCK.
    Figure 2.71: GenBank Searching Options
  4. If your DNA source file has entries in the features table that might be ambiguous, you will see a button that says Location Prefs…. Pressing this button will bring up Figure 2.72, allowing you to define how you want the feature locations to be interpreted. This window lists the possible ways in which various features are defined by NCBI for use in GenBank files. Some of these are not directly translatable into GCK features, so you can define how you want to handle those situations in this window.
    Figure 2.72: Location Preferences Dialog

Feel free to try different operations using the Deluxe Importer. The searching works the same way as an Entrez search would work at the NCBI web site.

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One Comment

  1. Posted February 29, 2012 at 11:18 am | Permalink

    Some truly good articles on this internet site , thanks for contribution.

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