Stochastic Modeling of Codon Bias with PRISM
T.E. Pronk, E.P. de Vink, D. Bosnacki and T.M. Breit

We present a biological case study of codon bias with the
probabilistic model checker PRISM with which we perform a
quantitative analysis of expression speeds of genes. The variability
in this setting concerns the matching of codons and anticodons. We
distinguish between iso-acceptance (one codon matches exactly one
anticodon) and wobble matching (multiple codons are matched by one
anticodon). Our modeling confirms a recent result by Lavner and
Kotlar, stating that at low and high expression speeds high codon
bias prevails, whereas at moderate expression speeds low codon bias
is more advantageous.  Although the approach needs further validation, 
our preliminary investigation shows that probabilistic model checking 
with PRISM is promising in obtaining further insight in codon bias.