Technical Note: Determining Peeling Order Using Sparse Matrix Algorithms

To study the effect of individual genes by segregation or linkage analyses, the likelihood of the model needs to be evaluated. The likelihood can be computed efficiently using the Elston-Stewart algorithm. This algorithm involves summing over the unobserved genotypes in the pedigree, which is called...

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Published in:Journal of dairy science Vol. 85; no. 6; pp. 1623 - 1629
Main Authors: Fernandez, S. A, Fernando, R. L
Format: Journal Article
Language:English
Published: Savoy, IL Am Dairy Sci Assoc 01.06.2002
American Dairy Science Association
Subjects:
Algorithms
Animal productions
Animals
Biological and medical sciences
Breeding
Cattle
Cattle - genetics
dairy cows
Female
Fundamental and applied biological sciences. Psychology
Genetic Linkage
genetics
Genotype
Likelihood Functions
linear models
Male
Mathematical Computing
Pedigree
recessive genes
Terrestrial animal productions
Vertebrates
Performance evaluation
Linkage
Monogeny
Genetic improvement
Sparse matrix
Model study
Simulation model
Milk production
Likelihood function
ISSN:0022-0302, 1525-3198
Online Access:Get full text
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Summary:To study the effect of individual genes by segregation or linkage analyses, the likelihood of the model needs to be evaluated. The likelihood can be computed efficiently using the Elston-Stewart algorithm. This algorithm involves summing over the unobserved genotypes in the pedigree, which is called peeling. An important aspect of this algorithm is to determine the order of peeling to maximize efficiency. This paper shows how determining peeling order is related to a problem in solving systems of symmetric sparse linear equations. It also shows how algorithms developed to efficiently solve those systems, can be used to determine the optimal order of peeling in the Elston-Stewart algorithm.
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ISSN:0022-0302
1525-3198
DOI:10.3168/jds.S0022-0302(02)74233-1