The Options screen is the third of four screens in the BLAST Search wizard, and has two tabs: Selection and Matches. These tabs allow you to customize miscellaneous parameters relating to the BLAST search.

  • Click the Selection tab to make it active.

    In the Selection tab:

    • To filter the database you’re searching using a text term, enter a text string in the Entrez query field.

    • To filter low-complexity regions in the query, check the box next to Ignore low complexity in query sequence. The blastn search program will use DUST for filtering; all other programs will use SEG.

    • To mask the query while producing seeds used to scan database (but not for extensions), check the box by Ignore low complexity during database lookup.

    • To mask any letters that were lower-case in the FASTA input, check the box next to Ignore lower case letters.

  • Click the Matches tab to make it active.

    In the Matches tab:

    • Enter a number next to Maximum sequences, the maximum number of aligned sequences to display. The actual number of alignments may be greater than this number. The default is 100.

    • Enter a number beside Expect threshold, the expected number of chance matches in a random model. The default is 10.

    • Enter a number next to Maximum regional matches to limit the number of matches to a query range. The default is 0.

To learn about the optional tools in the bottom left corner of the screen, see the bottom of this topic.

Once you have made the desired selections, do any of the following:

  • To continue filtering, press Next to continue to the Job screen.
  • To start the search immediately, press the Run Now button () or Run button. The Jobs panel in the application will open and contain information on the status of the search. During the search, a progress dialog is displayed where you can cancel the search using the Stop button, hide the dialog using the Hide button, or set up another query using the Settings… button. Use the Jobs panel to monitor an online search, stop an in-progress search, or open search results in the Text, Table and Pairwise views.
  • To close the Search wizard without starting a search, press Cancel.

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