Computational Modelling of the Interruptional Activities between Transposable Elements

Abstract

Transposable elements (TEs) are DNA sequences that can either move or copy themselves to new positions within a genome. They constitute approximately 45% of the human genome. Knowing the evolution of TEs is helpful in understanding the activities of these elements and their impacts on genomes. In this paper, we devise a formal model providing notations/definitions that are compatible with biological nomenclature, while still providing a suitable formal foundation for computational analysis. We define sequential interruptions between TEs that occur in a genomic sequence to estimate how often TEs interrupt other TEs, useful in predicting their ages. We also define the recursive interruption context-free grammar to capture the recursive nature in which TEs nest themselves into other TEs. We then associate probabilities to convert the context-free grammar into a stochastic context-free grammar, and discuss how to use the CYK algorithm to find a most likely parse tree predicting TE nesting.