Classifying Cytochrome c Oxidase subunit 1 by translation initiation mechanism using side effect machines

Abstract

Cytochrome c oxidase subunit 1 (cox1) is unusual among mitochondrial genes in that instead of using AUG or one of the recognized alternative start codons it often appears to use an unknown means for initiating translation. However, the frequency of this unusual behavior as well as the underlying molecular mechanism are unknown. In this paper we use side effect machines to probe for signal in the sequence. Evolved side effect machines were able to correctly classify cox1 genes with ambiguous start codons 80.1% of the time. Side effect machines are finite state machines that have side effects associated with their states. In this study a simple side effect, a counter for the number of times the state was entered, is used. The problem is found to be challenging, a substantial majority of replicates found no signal, but some classifiers with statistically significant classification ability were located.