Retrieving BLAST results

The BLAST search results dialog box allows you to retrieve and store the results of BLAST queries submitted using GeneStudio's BLAST interface, to view the search results, and to download hit sequences directly into GeneStudio components.

Note: Downloaded results are stored in XML format on your computer in the folder [APPLICATION_DATA]\GeneStudio\blast_results. [APPLICATION_DATA] is a system-defined folder.

To view the BLAST results dialog box, select the BLAST results menu item from the Internet menu.  The BLAST results dialog box contains a list box with information about BLAST queries that have been submitted using GeneStudio's BLAST search function.

 

Retrieving the results of a BLAST query:
Before a search result can be viewed, it must be downloaded from the BLAST server.  Once a search result has been downloaded, it will be available for viewing until you decide to delete it.  Searches that have been submitted but not yet downloaded are denoted as Submitted in the status column of the results list.  To retrieve the result, click on a search name and press the Refresh button.  If the search is completed, the result will be downloaded from the BLAST server to your computer and the status will be changed to Retrieved.  If the search result is no longer on the BLAST server, the status will be changed to Unknown.

Viewing the search result:
The BLAST results dialog provides two commands for viewing search results.  The Classic view button provides a view of the results formatted as an HTML page.  This page resembles the online BLAST search page.  The View results button calls the BLAST results viewer dialog box, which is used to download hit sequences.  For more information on the BLAST Results viewer dialog box, see the BLAST results viewer reference in the table below.  To view a result, click on its name in the Results list and then press the Classic view or View results button.

Downloading hit sequences:
To download hit sequences, click on the name of the search to be viewed and then press the View results button. The BLAST results viewer dialog box will be displayed.  This dialog box lists the sequences with check boxes beside the sequence name.  Select sequences for download using the check boxes.  Selected sequences can be saved to disk or they can be saved and opened in SeqVerter or the Alignment editor.

Deleting a search result:
To delete a search result, click on the search name in the results list, and then press the Delete results button.


BLAST results viewer reference table.

The BLAST results viewer dialog box is presented when you press the View results button.  This dialog allows you to download sequences, view hit details and view the GenBank entry for the hit sequence.

Hit sequence list

  • List box
    List of BLAST hit results.  The sequence name and definition line are displayed.  The identity score is displayed in parentheses.  Check boxes beside the sequence names are used to select sequences for downloading.  Double-click on the sequence name to view the NCBI GenBank entry for this sequence in your Web browser.
  • Select all
    Select all sequence in the results list for downloading.
  • Deselect all
    Deselect all sequence in the results list for downloading.
  • View in browser
    View the NCBI GenBank entry for the highlighted sequence in your web browser.
  • Hit details
    Display alignment for the highlighted sequence.

Options

  • Save only
    Download the selected sequences without opening them.
  • Save and open in SeqVerter
    Download the selected files and then open them in SeqVerter.
  • Save and open in the Alignment editor
    Download the selected files and then open them in the Alignment Editor.

Download folder

  • Edit box
    Enter the folder path for downloaded files.
  • Browse button
    Select the download folder using the Browser for folder dialog box.
  • Import folder
    Use the default import folder.
  • Export folder
    Use the default export folder.
  • Last folder used
    Use the last folder visited.

File names

  • Locus
    Use the hit sequence locus name for the downloaded file name.
  • Accession number
    Use the hit sequence accession number for the downloaded file name.

Action

  • Exit
    Close this dialog box.
  • Import and exit
    Close this dialog box and the BLAST search results dialog box after downloading.
  • Import and return to BLAST results
    Close this dialog box and return to the BLAST search results dialog box after downloading.
  • Cancel download
    Abort the current download.