Pablo A S Fonseca1, Aroa Suárez-Vega1, Gabriele Marras1,2, Ángela Cánovas1. 1. University of Guelph, Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, 50 Stone Rd E, Guelph N1G 2W1, ONT, Canada. 2. The Semex Alliance, 5653 ON-6, Guelph N1G 3Z2, ONT, Canada.
Abstract
BACKGROUND: The development of high-throughput sequencing and genotyping methodologies has enabled the identification of thousands of genomic regions associated with several complex traits. The integration of multiple sources of biological information is a crucial step required to better understand patterns regulating the development of these traits. FINDINGS: Genomic Annotation in Livestock for positional candidate LOci (GALLO) is an R package developed for the accurate annotation of genes and quantitative trait loci (QTLs) located in regions identified in common genomic analyses performed in livestock, such as genome-wide association studies and transcriptomics using RNA sequencing. Moreover, GALLO allows the graphical visualization of gene and QTL annotation results, data comparison among different grouping factors (e.g., methods, breeds, tissues, statistical models, studies), and QTL enrichment in different livestock species such as cattle, pigs, sheep, and chickens. CONCLUSIONS: Consequently, GALLO is a useful package for annotation, identification of hidden patterns across datasets, and data mining previously reported associations, as well as the efficient examination of the genetic architecture of complex traits in livestock.
BACKGROUND: The development of high-throughput sequencing and genotyping methodologies has enabled the identification of thousands of genomic regions associated with several complex traits. The integration of multiple sources of biological information is a crucial step required to better understand patterns regulating the development of these traits. FINDINGS: Genomic Annotation in Livestock for positional candidate LOci (GALLO) is an R package developed for the accurate annotation of genes and quantitative trait loci (QTLs) located in regions identified in common genomic analyses performed in livestock, such as genome-wide association studies and transcriptomics using RNA sequencing. Moreover, GALLO allows the graphical visualization of gene and QTL annotation results, data comparison among different grouping factors (e.g., methods, breeds, tissues, statistical models, studies), and QTL enrichment in different livestock species such as cattle, pigs, sheep, and chickens. CONCLUSIONS: Consequently, GALLO is a useful package for annotation, identification of hidden patterns across datasets, and data mining previously reported associations, as well as the efficient examination of the genetic architecture of complex traits in livestock.
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