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Evolutionary Genomics Group Department of Computational Molecular Biology |
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Authors: Peter F Arndt, Terence Hwa Title: Identification and measurement of neighbor-dependent nucleotide substitution processes Abstract: MOTIVATION: Neighbor-dependent substitution processes generated specific pattern of dinucleotide frequencies in the genomes of most organisms. The CpG-methylation-deamination process is; e.g. 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 developed a method that is able to identify the most relevant neighbor-dependent substitution processes; estimate their relative frequencies and judge their importance in order to be included into the modeling. Starting from a model for neighbor independent nucleotide substitution we successively added 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. AVAILABILITY: A web server to perform the presented analysis is freely available at: http://evogen.molgen.mpg.de/server/substitution-analysis Reference: Bioinformatics (Oxford; England) 21 (2005) 2322-8 Links: [Journal] [Fulltext (pdf)] |