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Abstract

Motivation: Neighbor dependent substitution processes generated specific pattern of dinucleotide frequencies in the genomes of most organisms. The CpG-methylation-deamination process is, for example, a prominent process in vertebrates (CpG-effect). Such processes, often with unknown mechanistic origins, need to be incorporated into realistic models of nucleotide substitutions. Results: Based on a general framework of nucleotide substitutions we develop a method that is able to identify the most relevant neighbor dependent substitution processes, estimate their relative frequencies, and judge their importance to be included into the modeling. Starting from a model for neighbor independent nucleotide substitution we successively add neighbor dependent substitution processes in the order of their ability to increase the likelihood of the model describing given data. The analysis of neighbor dependent nucleotide substitutions based on repetitive elements found in the genomes of human, zebrafish and fruit fly is presented.