title: Probabilistic whole-genome alignments reveal high indel rates in the human and mouse genomes.
abstract: BACKGROUND
  The two mutation processes that have the largest impact on genome evolution at small scales are substitutions, and sequence insertions and deletions (indels). While the former have been studied extensively, indels have received less attention, and in particular, the problem of inferring indel rates between pairs of divergent sequence remains unsolved. Here, I describe a novel and accurate method for estimating neutral indel rates between divergent pairs of genomes.
  
  
  RESULTS
  Simulations suggest that new method for estimating indel rates is accurate to within 2%, at divergences corresponding to that of human and mouse. Applying the method to these species, I show that indel rates are up to twice higher than is apparent from alignments, and depend strongly on the local G + C content. These results indicate that at these evolutionary distances, the contribution of indels to sequence divergence is much larger than hitherto appreciated. In particular, the ratio of substitution to indel rates between human and mouse appears to be around gamma = 8, rather than the currently accepted value of about gamma = 14.
authors.affiliation: MRC Functional Genetics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX1 3QX, United Kingdom. Gerton.lunter@dpag.ox.ac.uk
authors.forename: Gerton
authors.initials: G
authors.lastname: Lunter
mesh_terms: D000465:Algorithms; D000818:Animals; D001482:Base Composition / Q000235:genetics; D001483:Base Sequence; D002874:Chromosome Mapping / Q000379:methods*; D004252:DNA Mutational Analysis / Q000379:methods; D004251:DNA Transposable Elements / Q000235:genetics*; D019143:Evolution, Molecular; D017353:Gene Deletion; D016678:Genome / Q000235:genetics*; D015894:Genome, Human / Q000235:genetics; D006801:Humans; D051379:Mice; D008957:Models, Genetic; D015233:Models, Statistical; D008969:Molecular Sequence Data; D009154:Mutation / Q000235:genetics; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D004251:DNA Transposable Elements