Mutagenesis

The flow diagram shows the basic work flow for directed evolution of a gene. After plating the cells, each cell will grow into a colony. During cell growth, the error prone polymerase is not turned off so the colony grown up for sequencing will also contain mutations which could interfere with sequencing. The aim of this model is to determine the error rate at which a standard size colony would become too diverse for the sequence of the initial cell to be determined. A probabilistic matlab model was created to simulate the mutation process that occurs as a single cell grows into a colony. The model begins with the root of a binary tree which represents the single cell being grown into a colony. The basics of the model is illustrated below.

Afterwards for every base, the ratio of mutated to un-mutated cells is obtained. For our demonstration, a 20% cut off was used. When 20% of a base in the colony is mutated, the original base is determined to be retrievable from a sequencer. The graphs below plot the number of un-readable bases in a 1000bp gene against the polymerase error rate. The number of un-readable bases is averaged over 500 trials. A polymerase error rate of 0.1 would mean there is a 10% chance for a each and every base to be mutated on each cell replication.