Paper Info
Title
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.
Year
DOI
Venue
2013
10.1007/978-3-642-45008-2_9
Lecture Notes in Computer Science
Keywords
Field
DocType
transposable elements,stochastic context-free grammars,interruptional analysis,formal modelling
Genome,Interrupt,Parse tree,CYK algorithm,Transposable element,Computer science,Grammar,Theoretical computer science,Human genome,Recursion
Conference
Volume
ISSN
Citations 
8273
0302-9743
0
PageRank 
References 
Authors
0.34
1
2
Name
Order
Citations
PageRank
Lingling Jin117510.96
Ian McQuillan29724.72