On optimal primer design for identifying novel molecular sequences in biodiversity studies
M. Newton, Y. Lee, M. Chelius and E. Triplett
Abstract
Small subinit ribosomal RNAs (SSU rRNAs) are molecular
sequences which exist in every living organism. Being highly conserved
throughout evolution, they form the basis of experiments to
identify unknown organisms, for instance those living in
extreme environments. Statistical decision theory naturally addresses
the problem of how to design primers in such experiments;
primers are short sequences complementary to part of the
unknown target sequence and they are required for sequence
amplification by PCR (polymerase chain reaction).
Known SSU rRNA sequences, their phylogeny, and a substitution
model of evolution enter the Bayesian optimal design calculation.