RAMHA: a PC-based Monte-Carlo simulation of random saturation mutagenesis.

Random mutagenesis is a powerful tool in protein structure-function analyses. One approach to random mutagenesis is the de novo synthesis of polypeptide-encoding oligodeoxy-nucleotides using doped nucleoside phosphoramidites. A Turbo PASCAL program, RAMHA, is described for modeling such mutagenesis. Upon entering the target sequence and the desired level of nucleotide contamination, RAMHA performs a Monte Carlo simulation of the mutagenesis, compiling statistics on the similarity of resultant mutant polypeptides to the wild-type sequence, the frequency of premature open-reading frame terminations, and other relevant outcomes. Simulated mutagenesis of two DNA targets has led to the development of two different strategies to avoid the random introduction of stop codons within mutagenized gene segments.