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.

中文翻译：

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GALLO：用于基因组注释和整合家畜中多个数据源的 R 包，用于位置候选位点

摘要

背景

高通量测序和基因分型方法的发展使得能够识别与几个复杂性状相关的数千个基因组区域。整合多个生物信息源是更好地理解调节这些性状发展的模式所需的关键步骤。

发现

家畜基因组注释位置候选 LOci (GALLO) 是一个 R 包，用于准确注释基因和数量性状基因座 (QTL)，这些基因和数量性状位点 (QTL) 位于家畜常见基因组分析中确定的区域，例如全基因组关联研究和转录组学使用 RNA 测序。此外，GALLO 允许基因和 QTL 注释结果的图形可视化，不同分组因素（例如，方法、品种、组织、统计模型、研究）之间的数据比较，以及不同牲畜物种（如牛、猪、羊、和鸡。

结论

因此，GALLO 是一个有用的包，用于注释、跨数据集的隐藏模式识别和数据挖掘以前报告的关联，以及有效检查牲畜复杂性状的遗传结构。