The  BLAST Genomes search box, located on the BLAST ® (Basic Local Alignment Search Tool) home page (Figure 1) allows you to set up a BLAST search against the best genome assembly available for an organism. Use these steps:

• Begin typing the name of the organism (for example "American") to invoke the organism listing.
• Select the matching name (taxid) for the organism from the listing, for example "American Alligator (taxid: 8496)"
• Click the Search button. 

Figure 1: A part of the BLAST ® home page that includes the BLAST Genomes search box

The resulting BLAST page will have the Database menu only for the sequences related to the American Alligator reference assembly, rAllMis1.

Figure 2: Genome-specific blastn page. The Search Set Database menu is displaying the databases associated with the selected genome assembly

To compare your sequence(s) against the genome, proceed as you would for any other blastn search, by entering your query sequence(s) in the search box as accession numbers or in the FASTA format.

While BLAST will select the best assembly, there can be more than one assembly for the organism. To see what assemblies are available and to run BLAST against the one you want:  

• Search the NCBI Datasets Genome site with organism of your interest (for example, Alligator mississippiensis ). 
• Access the record that you want, for example Algmis_Hirise_1.0.
• Use BLAST the genome link located at the top of the record and that will load the blastn suite for this specific assembly. 

What happens if there is no genome assembly for the organism of your interest?

You can still still use the BLAST Genomes search box to search with your organism. BLAST will present the standard blastn suite with the added organism limit for your organism.