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To make a request to a local BLAST database do the following:

  • If you’re using BLAST open Tools ‣ BLAST ‣ BLAST Search.
  • If you’re using BLAST+ open Open Tools ‣ BLAST ‣ BLASTOpen Tools ‣ BLAST+ ‣ BLAST+ Search.

If there is a sequence opened you can also initiate the request to a local BLAST database from the Sequence View:

  • If you’re using BLAST select the Analyze ‣ Query with BLAST item in the context menu or in the Actions main menu.
  • If you’re using BLAST+ select the  Select the Analyze ‣ Query with BLAST+ item in the context menu or in the Actions the main menu.

The Request to local BLAST+ database dialog will appear:


Megablast - select this option to compare query queries with closely related sequences. It works best if the target percent identity is 95% or more, but it is very fast.


The view of the Advanced options tab depends on the selected search. For the blastn search, it looks like on in the picture above. When the blastx search is selected in the general options, the view of the Advanced options tab is the following:


Matrix — key element in evaluating the quality of a pair-wise sequence alignment is the “substitution matrix”, which assigns a score for aligning any possible pair of residues.