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Context dependent substitution biases vary within the human genome

dc.contributor.author Nevarez, P Andrew
dc.contributor.author DeBoever, Christopher M
dc.contributor.author Freeland, Benjamin J
dc.contributor.author Quitt, Marissa A
dc.contributor.author Bush, Eliot C
dc.date.accessioned 2011-06-21T17:27:56Z
dc.date.available 2011-06-21T17:27:56Z
dc.date.issued 2010
dc.identifier.citation Nevarez,P. Andrew;DeBoever,Christopher M.;Freeland,Benjamin J.;Quitt,Marissa A.;Bush,Eliot C.. 2010. Context dependent substitution biases vary within the human genome. Bmc Bioinformatics 11( ): 462-462.
dc.identifier.issn 1471-2105
dc.identifier.uri https://hdl.handle.net/10161/4335
dc.description.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.
dc.language.iso en_US
dc.publisher Springer Science and Business Media LLC
dc.relation.isversionof 10.1186/1471-2105-11-462
dc.subject dna-sequence evolution
dc.subject nucleotide substitution
dc.subject maximum-likelihood
dc.subject noncoding regions
dc.subject methylation
dc.subject rates
dc.subject patterns
dc.subject oligonucleotides
dc.subject cpg
dc.subject biochemical research methods
dc.subject biotechnology & applied microbiology
dc.subject mathematical & computational biology
dc.title Context dependent substitution biases vary within the human genome
dc.title.alternative
dc.type Other article
dc.description.version Version of Record
duke.date.pubdate 2010-9-15
duke.description.issue
duke.description.volume 11
dc.relation.journal Bmc Bioinformatics
pubs.begin-page 462


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