Permutation Sorting Games

Ciliates have an unusual genome maintenance system. They host both an encrypted version and a decrypted version of their genomes. The decrypted version is often replaced by a newly decrypted copy of the encrypted version.The mathematical model for decryption postulates two permutation sorting operations for performing the decryption. These permutations are referred to as Context Directed Reversals[CDR] and Context Directed Swaps[CDS]. Not all permutations are sortable by these two operations. Even the sortable ones may require very specific sorting strategies for successful sorting.We are developing a computational tool which implements the sorting process as a game. This will allow us to quickly and accurately collect data regarding successful strategies. We hope that through an analysis of successful strategies we may garner a better understanding as to how this unique process evolved in Ciliates