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Old 09-10-2015, 09:34 AM   #2
Brian Bushnell
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Location: Walnut Creek, CA

Join Date: Jan 2014
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This sounds like a good place to use BBDuk, depending on what exactly you're trying to do.

bbduk.sh in=16S.fasta out=matching.fasta literal=CCTACGGGNGGCWGCAG k=17 mm=f copyundefined=t

That will give you all sequences that contain the literal, after first making copies of the literal to represent every fully-specified (ACGT) version of the degenerate bases. You can then run it a second time with the other primer and a different value of k (which should equal the primer length).
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