Descrambling Order Analysis in Ciliates

摘要

Certain genera of ciliates undergo a large genomic transformation, where many segments get rearranged and removed. A topic of interest is to predict a (partial) order on the rearrangement of segments to descramble. Similar to phylogenetic analysis, this prediction can be based on the principle of parsimony, whereby the smallest sequence of operations is likely close to the actual number. The Oxytricha trifallax genome is analyzed, providing evidence that multiple parallel recombination operations occur during descrambling, with alignment of interleaving segments in a manner that can be captured with the shuffle operation. Two similar systems involving shuffle are created, an optimal algorithm for each is created, and executed on the genomic data. One system can descramble 96.63% of the scrambled micronuclear chromosome fragments by 1 or 2 applications of shuffle, and every sequence can be descrambled with at most seven operations.