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Does Primaclade accept IUPAC ambiguity codes?

April 26, 2017Ambiguity IUPAC primaclade

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Does Primaclade accept IUPAC ambiguity codes?

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Primaclade clade does not use IUPAC ambiguity codes when searching for primers only when reporting the consensus sequence. Currently Primaclade takes all IUPAC ambiguity codes (and any other nucleotide information that it does not recognize) and converts it into an “N” before feeding the sequence into the Primer3 algorithm. This is actually a limitation of Primer3, and since Primaclade is built on top of Primer3 it inherits this problem as well.