Obtain "in silico" amplicon

[TinySci]

From the available genomes online, how can I obtain the amplicon produced by a specific primer? There are some strains I don't have in the lab and was hoping to assess the amplicon in silico.

Is there a way to use BLAST for this?


Thank you!

[m_two]

If you concatenate the forward and reverse complement of the reverse primer sequence into a single sequence then this blast command should return all possible products up to 2kb in size. Adjust hspsepSmax to the size of your liking.

blastn reference_database.fasta primers-fwd-rev-revcomp.fasta M=1 N=-3 Q=3 R=3 hspsepSmax=2000 topcomboN=3 B=3 V=3

[TinySci]

Thanks, m_two!

What about primer-BLAST? Will this show the amplicon product too?