CaltechAUTHORS
  A Caltech Library Service

Context dependent substitution biases vary within the human genome

Nevarez, P. Andrew and DeBoever, Christopher M. and Freeland, Benjamin J. and Quitt, Marissa A. and Bush, Eliot C. (2010) Context dependent substitution biases vary within the human genome. BMC Bioinformatics, 11 . Art. No. 462. ISSN 1471-2105. https://resolver.caltech.edu/CaltechAUTHORS:20101029-095951501

[img]
Preview
PDF - Published Version
Creative Commons Attribution.

315Kb
[img]
Preview
PDF (Proof of relative abundance algorithm by mathematical induction.) - Supplemental Material
Creative Commons Attribution.

142Kb
[img]
Preview
PDF (Effect of sample size on total context bias calculation.) - Supplemental Material
Creative Commons Attribution.

1263Kb
[img] Other (Table of top context bias values for 2-5 bp single substitution patterns.) - Supplemental Material
Creative Commons Attribution.

32Kb
[img]
Preview
PDF (Comparison of context bias after removing CpG-containing patterns.) - Supplemental Material
Creative Commons Attribution.

13Kb
[img]
Preview
PDF (Unweighted total context bias in tranposons and non-repetitive sequence. ) - Supplemental Material
Creative Commons Attribution.

46Kb
[img]
Preview
PDF (Distribution of context bias differences between human lineage data sets.) - Supplemental Material
Creative Commons Attribution.

624Kb

Use this Persistent URL to link to this item: https://resolver.caltech.edu/CaltechAUTHORS:20101029-095951501

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.


Item Type:Article
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.1186/1471-2105-11-462DOIUNSPECIFIED
http://www.biomedcentral.com/1471-2105/11/462PublisherUNSPECIFIED
Additional Information:© 2010 Nevarez et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Received: 2 April 2010; Accepted: 15 September 2010; Published: 15 September 2010. We would like to thank Ran Libeskind-Hadas, Daniel Fielder, Lynn Bush and Steve Adolph for helpful discussions. Support for this work was provided by the NSF (MCB-0918335) and by and an institutional grant to Harvey Mudd College from the Howard Hughes Medical Institute. Authors’ contributions: PAN carried out the analysis and wrote the manuscript. CMD, BAF and MAQ carried out the analysis. ECB designed the project, carried out the analysis, and wrote the manuscript. All authors read and approved the final paper.
Funders:
Funding AgencyGrant Number
NSFMCB-0918335
Howard Hughes Medical InstituteUNSPECIFIED
Record Number:CaltechAUTHORS:20101029-095951501
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20101029-095951501
Official Citation:Nevarez et al.: Context dependent substitution biases vary within the human genome. BMC Bioinformatics 2010 11:462.
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:20598
Collection:CaltechAUTHORS
Deposited By: Jason Perez
Deposited On:01 Nov 2010 16:46
Last Modified:03 Oct 2019 02:12

Repository Staff Only: item control page