Cargando…

Assessment of the performance of hidden Markov models for imputation in animal breeding

BACKGROUND: In this paper, we review the performance of various hidden Markov model-based imputation methods in animal breeding populations. Traditionally, pedigree and heuristic-based imputation methods have been used for imputation in large animal populations due to their computational efficiency,...

Descripción completa

Detalles Bibliográficos
Autores principales:	Whalen, Andrew, Gorjanc, Gregor, Ros-Freixedes, Roger, Hickey, John M.
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	BioMed Central 2018
Materias:	Research Article
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6142395/ https://www.ncbi.nlm.nih.gov/pubmed/30223768 http://dx.doi.org/10.1186/s12711-018-0416-8

Ejemplares similares

Evaluation of sequencing strategies for whole-genome imputation with hybrid peeling
por: Ros-Freixedes, Roger, et al.
Publicado: (2020)

Hybrid peeling for fast and accurate calling, phasing, and imputation with sequence data of any coverage in pedigrees
por: Whalen, Andrew, et al.
Publicado: (2018)

Accuracy of whole-genome sequence imputation using hybrid peeling in large pedigreed livestock populations
por: Ros-Freixedes, Roger, et al.
Publicado: (2020)

AlphaFamImpute: high-accuracy imputation in full-sib families from genotype-by-sequencing data
por: Whalen, Andrew, et al.
Publicado: (2020)

Family-specific genotype arrays increase the accuracy of pedigree-based imputation at very low marker densities
por: Whalen, Andrew, et al.
Publicado: (2019)

A method for allocating low-coverage sequencing resources by targeting haplotypes rather than individuals
por: Ros-Freixedes, Roger, et al.
Publicado: (2017)

Evaluation of vicinity-based hidden Markov models for genotype imputation
por: Wang, Su, et al.
Publicado: (2022)

A method for the allocation of sequencing resources in genotyped livestock populations
por: Gonen, Serap, et al.
Publicado: (2017)

Extending long-range phasing and haplotype library imputation algorithms to large and heterogeneous datasets
por: Money, Daniel, et al.
Publicado: (2020)

Genomic prediction with whole-genome sequence data in intensely selected pig lines
por: Ros-Freixedes, Roger, et al.
Publicado: (2022)

A Strategy To Exploit Surrogate Sire Technology in Livestock Breeding Programs
por: Gottardo, Paolo, et al.
Publicado: (2018)

Genetic variation in recombination rate in the pig
por: Johnsson, Martin, et al.
Publicado: (2021)

A hybrid method for the imputation of genomic data in livestock populations
por: Antolín, Roberto, et al.
Publicado: (2017)

Impact of index hopping and bias towards the reference allele on accuracy of genotype calls from low-coverage sequencing
por: Ros-Freixedes, Roger, et al.
Publicado: (2018)

Rare and population-specific functional variation across pig lines
por: Ros-Freixedes, Roger, et al.
Publicado: (2022)

Incorporating periodic variability in hidden Markov models for animal movement
por: Li, Michael, et al.
Publicado: (2017)

AlphaMate: a program for optimizing selection, maintenance of diversity and mate allocation in breeding programs
por: Gorjanc, Gregor, et al.
Publicado: (2018)

Spatial modelling improves genetic evaluation in smallholder breeding programs
por: Selle, Maria L., et al.
Publicado: (2020)

AlphaSimR: an R package for breeding program simulations
por: Gaynor, R Chris, et al.
Publicado: (2020)

Inference in Hidden Markov Models
por: Cappe, Olivier
Publicado: (2005)

Hidden Markov Modeling with HMMTeacher
por: Fuentes-Beals, Camilo, et al.
Publicado: (2022)

Phasing and imputation of single nucleotide polymorphism data of missing parents of biparental plant populations
por: Gonen, Serap, et al.
Publicado: (2021)

Hidden Markov models: estimation and control
por: Elliott, Robert J, et al.
Publicado: (1995)

Sequence variation, evolutionary constraint, and selection at the CD163 gene in pigs
por: Johnsson, Martin, et al.
Publicado: (2018)

Parentage assignment with genotyping‐by‐sequencing data
por: Whalen, Andrew, et al.
Publicado: (2018)

Hidden Markov Model Variants and their Application
por: Winters-Hilt, Stephen
Publicado: (2006)

A heuristic method for fast and accurate phasing and imputation of single-nucleotide polymorphism data in bi-parental plant populations
por: Gonen, Serap, et al.
Publicado: (2018)

Error statistics of hidden Markov model and hidden Boltzmann model results
por: Newberg, Lee A
Publicado: (2009)

Scalable Bayesian Inference for Coupled Hidden Markov and Semi-Markov Models
por: Touloupou, Panayiota, et al.
Publicado: (2019)

Scanpath modeling and classification with hidden Markov models
por: Coutrot, Antoine, et al.
Publicado: (2017)

Modelling reassurances of clinicians with hidden Markov models
por: Popov, Valentin, et al.
Publicado: (2019)

Performance of Hidden Markov Models in Recovering the Standard Classification of Glycoside Hydrolases
por: Rossi, Mariana Fonseca, et al.
Publicado: (2017)

The potential of shifting recombination hotspots to increase genetic gain in livestock breeding
por: Gonen, Serap, et al.
Publicado: (2017)

Epitope Discovery with Phylogenetic Hidden Markov Models
por: Lacerda, Miguel, et al.
Publicado: (2010)

Estimating Empirical Codon Hidden Markov Models
por: De Maio, Nicola, et al.
Publicado: (2013)

Initiating maize pre-breeding programs using genomic selection to harness polygenic variation from landrace populations
por: Gorjanc, Gregor, et al.
Publicado: (2016)

Effect of manipulating recombination rates on response to selection in livestock breeding programs
por: Battagin, Mara, et al.
Publicado: (2016)

Hidden Markov Models: The Best Models for Forager Movements?
por: Joo, Rocio, et al.
Publicado: (2013)

A hidden Markov movement model for rapidly identifying behavioral states from animal tracks
por: Whoriskey, Kim, et al.
Publicado: (2017)

A genome-wide association study for loin depth and muscle pH in pigs from intensely selected purebred lines
por: Desire, Suzanne, et al.
Publicado: (2023)

Cannot write session to /tmp/vufind_sessions/sess_uount7k79ovo89jfvm3m7msm5g