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06-11-2015, 02:41 AM
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#1 |
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Junior Member
Location: Spain Join Date: May 2015
Posts: 5
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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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06-15-2015, 07:44 AM
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#2 |
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Member
Location: USA Join Date: Mar 2010
Posts: 50
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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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06-16-2015, 07:38 AM
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#3 |
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Junior Member
Location: Spain Join Date: May 2015
Posts: 5
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Thanks, m_two!
What about primer-BLAST? Will this show the amplicon product too? |
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