PDF(Pubmed)
Abstract：
Comprehensive and accurate genome annotation is crucial for inferring the predicted functions of an organism. Numerous tools exist to annotate genes, gene clusters, mobile genetic elements, and other diverse features. However, these tools and pipelines can be difficult to install and run, be specialized for a particular element or feature, or lack annotations for larger elements that provide important genomic context. Integrating results across analyses is also important for understanding gene function. To address these challenges, we present the Beav annotation pipeline. Beav is a command-line tool that automates the annotation of bacterial genome sequences, mobile genetic elements, molecular systems and gene clusters, key regulatory features, and other elements. Beav uses existing tools in addition to custom models, scripts, and databases to annotate diverse elements, systems, and sequence features. Custom databases for plant-associated microbes are incorporated to improve annotation of key virulence and symbiosis genes in agriculturally important pathogens and mutualists. Beav includes an optional Agrobacterium-specific pipeline that identifies and classifies oncogenic plasmids and annotates plasmid-specific features. Following the completion of all analyses, annotations are consolidated to produce a single comprehensive output. Finally, Beav generates publication-quality genome and plasmid maps. Beav is on Bioconda and is available for download at https://github.com/weisberglab/beav.
OBJECTIVE: Annotation of genome features, such as the presence of genes and their predicted function, or larger loci encoding secretion systems or biosynthetic gene clusters, is necessary for understanding the functions encoded by an organism. Genomes can also host diverse mobile genetic elements, such as integrative and conjugative elements and/or phages, that are often not annotated by existing pipelines. These elements can horizontally mobilize genes encoding for virulence, antimicrobial resistance, or other adaptive functions and alter the phenotype of an organism. We developed a software pipeline, called Beav, that combines new and existing tools for the comprehensive annotation of these and other major features. Existing pipelines often misannotate loci important for virulence or mutualism in plant-associated bacteria. Beav includes custom databases and optional workflows for the improved annotation of plant-associated bacteria. Beav is designed to be easy to install and run, making comprehensive genome annotation broadly available to the research community.
OBJECTIVE: Annotation of genome features, such as the presence of genes and their predicted function, or larger loci encoding secretion systems or biosynthetic gene clusters, is necessary for understanding the functions encoded by an organism. Genomes can also host diverse mobile genetic elements, such as integrative and conjugative elements and/or phages, that are often not annotated by existing pipelines. These elements can horizontally mobilize genes encoding for virulence, antimicrobial resistance, or other adaptive functions and alter the phenotype of an organism. We developed a software pipeline, called Beav, that combines new and existing tools for the comprehensive annotation of these and other major features. Existing pipelines often misannotate loci important for virulence or mutualism in plant-associated bacteria. Beav includes custom databases and optional workflows for the improved annotation of plant-associated bacteria. Beav is designed to be easy to install and run, making comprehensive genome annotation broadly available to the research community.
摘要：
全面而准确的基因组注释对于推断生物体的预测功能至关重要。存在许多工具来注释基因，基因簇，移动遗传元素，和其他多样化的特征。然而,这些工具和管道很难安装和运行，专门针对特定元素或特征，或缺少提供重要基因组背景的较大元素的注释。整合分析结果对于理解基因功能也很重要。为了应对这些挑战，我们介绍Beav注释管道。Beav是一个命令行工具，可以自动注释细菌基因组序列，移动遗传元素，分子系统和基因簇，关键监管功能，和其他元素。除了自定义模型之外，Beav还使用现有工具，脚本,和数据库来注释不同的元素，系统,和序列特征。结合了植物相关微生物的自定义数据库，以改善农业上重要的病原体和互生体中关键毒力和共生基因的注释。Beav包括任选的农杆菌特异性管道,其鉴定和分类致癌质粒并注释质粒特异性特征。完成所有分析后，注释被合并以产生单一的综合输出。最后,Beav生成出版物质量的基因组和质粒图谱。Beav位于Bioconda上，可从https://github.com/weisberglab/beav下载。
目的：基因组特征的注释，比如基因的存在及其预测的功能，或编码分泌系统或生物合成基因簇的较大基因座，是理解有机体编码的功能所必需的。基因组还可以承载不同的可移动遗传元件，如整合和共轭元件和/或噬菌体，通常不被现有管道注释。这些元件可以水平移动编码毒力的基因，抗菌素耐药性，或其他适应性功能并改变生物体的表型。我们开发了一个软件管道，叫Beav,它结合了新的和现有的工具，对这些和其他主要功能进行了全面的注释。现有的管道经常错误地注释对植物相关细菌中的毒力或共生很重要的基因座。Beav包括自定义数据库和可选的工作流程，用于改进植物相关细菌的注释。Beav的设计易于安装和运行，使全面的基因组注释广泛提供给研究界。
目的：基因组特征的注释，比如基因的存在及其预测的功能，或编码分泌系统或生物合成基因簇的较大基因座，是理解有机体编码的功能所必需的。基因组还可以承载不同的可移动遗传元件，如整合和共轭元件和/或噬菌体，通常不被现有管道注释。这些元件可以水平移动编码毒力的基因，抗菌素耐药性，或其他适应性功能并改变生物体的表型。我们开发了一个软件管道，叫Beav,它结合了新的和现有的工具，对这些和其他主要功能进行了全面的注释。现有的管道经常错误地注释对植物相关细菌中的毒力或共生很重要的基因座。Beav包括自定义数据库和可选的工作流程，用于改进植物相关细菌的注释。Beav的设计易于安装和运行，使全面的基因组注释广泛提供给研究界。
