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|Title:||BESSiE: a software for linear model BLUP and Bayesian MCMC analysis of large-scale genomic data||Contributor(s):||Boerner, Vinzent (author); Tier, Bruce (author)||Publication Date:||2016||Open Access:||Yes||DOI:||10.1186/s12711-016-0241-x||Handle Link:||https://hdl.handle.net/1959.11/21204||Open Access Link:||http://dx.doi.org/10.1186/s12711-016-0241-x||Abstract:||Background: The advent of genomic marker data has triggered the development of various Bayesian algorithms for estimation of marker effects, but software packages implementing these algorithms are not readily available, or are limited to a single algorithm, uni-variate analysis or a limited number of factors. Moreover, script based environments like R may not be able to handle large-scale genomic data or exploit model properties which save computing time or memory (RAM). Results: BESSiE is a software designed for best linear unbiased prediction (BLUP) and Bayesian Markov chain Monte Carlo analysis of linear mixed models allowing for continuous and/or categorical multivariate, repeated and missing observations, various random and fixed factors and large-scale genomic marker data. BESSiE covers the algorithms genomic BLUP, single nucleotide polymorphism (SNP)-BLUP, BayesA, BayesB, BayesCπ and BayesR for estimating marker effects and/or summarised genomic values. BESSiE is parameter file driven, command line operated and available for Linux environments. BESSiE executable, manual and a collection of examples can be downloaded http:// turing.une.edu.au/~agbu-admin/BESSiE/. Conclusion: BESSiE allows the user to compare several different Bayesian and BLUP algorithms for estimating marker effects from large data sets in complex models with the same software by small alterations in the parameter file. The program has no hard-coded limitations for number of factors, observations or genetic markers.||Publication Type:||Journal Article||Source of Publication:||Genetics Selection Evolution, v.48, p. 1-5||Publisher:||BioMed Central Ltd||Place of Publication:||United Kingdom||ISSN:||1297-9686||Field of Research (FOR):||060412 Quantitative Genetics (incl. Disease and Trait Mapping Genetics)
060411 Population, Ecological and Evolutionary Genetics
|Peer Reviewed:||Yes||HERDC Category Description:||C1 Refereed Article in a Scholarly Journal||Statistics to Oct 2018:||Visitors: 27
|Appears in Collections:||Journal Article|
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