title: Identification and measurement of neighbor-dependent nucleotide substitution processes.
abstract: BACKGROUND
  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.
  
  
  BACKGROUND
  A web server to perform the presented analysis is freely available at: http://evogen.molgen.mpg.de/server/substitution-analysis
authors.affiliation: Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany. arndt@molgen.mpg.de
authors.forename: Peter F
authors.initials: PF
authors.lastname: Arndt
authors.forename: Terence
authors.initials: T
authors.lastname: Hwa
mesh_terms: D000465:Algorithms; D000818:Animals; D001482:Base Composition; D020137:Base Pair Mismatch / Q000235:genetics*; D020029:Base Pairing / Q000235:genetics; D001483:Base Sequence; D002874:Chromosome Mapping / Q000379:methods*; D018899:CpG Islands / Q000235:genetics; D004331:Drosophila melanogaster; D019143:Evolution, Molecular; D015894:Genome, Human; D006801:Humans; D008957:Models, Genetic; D008969:Molecular Sequence Data; D009711:Nucleotides / Q000235:genetics*; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012689:Sequence Homology, Nucleic Acid; D012984:Software; D015027:Zebrafish
chemical_list: D009711:Nucleotides