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A Stochastic Model for Genomic Interspersed Duplication

Farnoud, Farzad and Schwartz, Moshe and Bruck, Jehoshua (2015) A Stochastic Model for Genomic Interspersed Duplication. California Institute of Technology , Pasadena, CA. (Unpublished) http://resolver.caltech.edu/CaltechAUTHORS:20150209-161532302

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Abstract

Mutation processes such as point mutation, insertion, deletion, and duplication (including tandem and interspersed duplication) have an important role in evolution, as they lead to genomic diversity, and thus to phenotypic variation. In this work, we study the expressive power of interspersed duplication, i.e., its ability to generate diversity, via a simple but fundamental stochastic model, where the length and the location of the subsequence that is duplicated and the point of insertion of the copy are chosen randomly. In contrast to combinatorial models, where the goal is to determine the set of possible outcomes regardless of their likelihood, in stochastic systems, we investigate the properties of the set of high-probability sequences. In particular we provide results regarding the asymptotic behavior of frequencies of symbols and short words in a sequence evolving through interspersed duplication. The study of such a systems is an important step towards the design and analysis of more realistic and sophisticated models of genomic mutation processes.


Item Type:Report or Paper (Technical Report)
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http://www.paradise.caltech.edu/papers/etr129.pdfAuthorReport
Group:Parallel and Distributed Systems Group
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ParadiseETR129
Record Number:CaltechAUTHORS:20150209-161532302
Persistent URL:http://resolver.caltech.edu/CaltechAUTHORS:20150209-161532302
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:54604
Collection:CaltechPARADISE
Deposited By: Kristin Buxton
Deposited On:10 Feb 2015 05:16
Last Modified:10 Feb 2015 05:16

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