title: Context dependent substitution biases vary within the human genome.
abstract: BACKGROUND
  Models of sequence evolution typically assume that different nucleotide positions evolve independently. This assumption is widely appreciated to be an over-simplification. The best known violations involve biases due to adjacent nucleotides. There have also been suggestions that biases exist at larger scales, however this possibility has not been systematically explored.
  
  
  RESULTS
  To address this we have developed a method which identifies over- and under-represented substitution patterns and assesses their overall impact on the evolution of genome composition. Our method is designed to account for biases at smaller pattern sizes, removing their effects. We used this method to investigate context bias in the human lineage after the divergence from chimpanzee. We examined bias effects in substitution patterns between 2 and 5 bp long and found significant effects at all sizes. This included some individual three and four base pair patterns with relatively large biases. We also found that bias effects vary across the genome, differing between transposons and non-transposons, between different classes of transposons, and also near and far from genes.
  
  
  CONCLUSIONS
  We found that nucleotides beyond the immediately adjacent one are responsible for substantial context effects, and that these biases vary across the genome.
authors.affiliation: Department of Biology, Harvey Mudd College, Claremont, CA, USA.
authors.forename: P Andrew
authors.initials: PA
authors.lastname: Nevarez
authors.forename: Christopher M
authors.initials: CM
authors.lastname: DeBoever
authors.forename: Benjamin J
authors.initials: BJ
authors.lastname: Freeland
authors.forename: Marissa A
authors.initials: MA
authors.lastname: Quitt
authors.forename: Eliot C
authors.initials: EC
authors.lastname: Bush
mesh_terms: D000818:Animals; D001482:Base Composition; D001483:Base Sequence; D019295:Computational Biology; D004251:DNA Transposable Elements; D015894:Genome, Human; D006801:Humans; D009711:Nucleotides / Q000235:genetics; D020641:Polymorphism, Single Nucleotide
chemical_list: D004251:DNA Transposable Elements; D009711:Nucleotides