A continuous analog of run length distributions reflecting accumulated fractionation events

BMC Bioinformatics

Research

David Sankoff¹  Zhe Yu¹ 

[1] Department of Mathematics and Statistics, University of Ottawa, 585 King Edward Avenue, K1N 6N5, Ottawa, Ontario, Canada;

关键词: Genomics;    Whole genome duplication;    Analysis of runs;    Probability modeling;    Duplicate gene deletion;   

DOI  :  10.1186/s12859-016-1265-5

来源: Springer

【 摘 要 】

BackgroundWe propose a new, continuous model of the fractionation process (duplicate gene deletion after polyploidization) on the real line. The aim is to infer how much DNA is deleted at a time, based on segment lengths for alternating deleted (invisible) and undeleted (visible) regions.ResultsAfter deriving a number of analytical results for “one-sided” fractionation, we undertake a series of simulations that help us identify the distribution of segment lengths as a gamma with shape and rate parameters evolving over time. This leads to an inference procedure based on observed length distributions for visible and invisible segments.ConclusionsWe suggest extensions of this mathematical and simulation work to biologically realistic discrete models, including two-sided fractionation.

【 授权许可】

CC BY   
© The Author(s) 2016

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