A model-independent approach to infer hierarchical codon substitution dynamics

Background: Codon substitution constitutes a fundamental process in molecular biology that has been studied extensively. However, prior studies rely on various assumptions, e.g. regarding the relevance of specific biochemical properties, or on conservation criteria for defining substitution groups. Ideally, one would instead like to analyze the substitution process in terms of raw dynamics, independently of underlying system specifics. In this paper we propose a method for doing this by identifying groups of codons and amino acids such that these groups imply closed dynamics. The approach relies on recently developed spectral and agglomerative techniques for identifying hierarchical organization in dynamical systems. Results: We have applied the techniques on an empirically derived Markov model of the codon substitution process that is provided in the literature. Without system specific knowledge of the substitution process, the techniques manage to "blindly" identify multip...

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: Olof Görnerup, Martin Nilsson Jacobi
• Keywords: Amino Acids, BMCBI 2010, Codon Substitution, Substitution Process