Finding homologous genes with primers designed using evolutionary models

Abstract

Genes homologous to a set of known, aligned, genes can be found by screening DNA libraries with PCR. PCR primers for such screens are commonly designed via a method described by Sells and Chernoff (1995). This standard design method does not make use of information about the evolutionary relationship between the known genes. The present study investigated the efficacy of using information about evolutionary relationships (inferred from the sequence data) in the design of PCR primers. This study compares the standard primer design method (represented herein by a modified multinomial distribution) with evolutionary model based primer design methods. The primer design method that, given an alignment of known sequences with one sequence left out, assigned a higher probability, on average, to the left-out sequence, was defined as the better method. By this measure of relative performance, an evolutionary model based primer design method sensitive to states correlated across sites of a sequence, outperformed the standard method, on the alignments studied.