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Old 06-11-2015, 02:41 AM   #1
TinySci
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Default Obtain "in silico" amplicon

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!
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Old 06-15-2015, 07:44 AM   #2
m_two
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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
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Old 06-16-2015, 07:38 AM   #3
TinySci
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Thanks, m_two!

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