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Bioinformatics Advance Access published online on March 16, 2009
Bioinformatics, doi:10.1093/bioinformatics/btp146
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© The Author (2009). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

A method and program for estimating graphical models for linkage disequilibrium that scale linearly with the number of loci, and their application to gene drop simulation

Alun Thomas

Department of Biomedical Informatics, University of Utah. Genetic Epidemiology, 391 Chipeta Way Suite D, Salt Lake City, UT 84108, USA

*To whom correspondence should be addressed. Alun Thomas, E-mail: alun{at}genepi.med.utah.edu


  Abstract

Motivation: Efficient models for genetic linkage disequilibrium are needed to enable appropriate statistical analysis of the dense, genome wide single nucleotide polymorphism assays currently available.

Results: Estimation of graphical models for linkage disequilibrium within a restricted class of decomposable models is shown to be possible using computer time and storage that scale linearly with the number of loci. Programs for estimation and for simulating from these models on a whole genome basis are described and provided.

Availability: Java classes and source code for IntervalLD and GeneDrops are freely available over the internet at http://bioinformatics.med.utah.edu/~alun.

Contact: alun{at}genepi.med.utah.edu

Associate Editor: Dr. Alex Bateman

Received on November 13, 2008; revised on February 5, 2009; accepted on March 11, 2009

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