Highly mutable organisms often challenge primer design for diagnostic PCR
kit manufacturers due to new mutations occurring in hybridization sites. Novel variants
may require reconsideration of the existing PCR primers and even result in
misdiagnosis. While conserved sequences are often the main target of primer design
algorithms, they often do not consider possible new mutants. We represent a
generalizable algorithm for filtration of the sequence to identify conserved sequences
and the less likely regions to mutate. Primers selected from the filtered sequences are
expected to target regions with lower mutation rates and consecutively act indifferent
to more variants of a target pathogen, providing long-lasting primers and less frequent
primer redesign.
Keywords: Molecular Evolution, Primer Picking Algorithms, Primer Selection,
Sequence Conservation.
