VIBES:用于注释和可视化细菌基因组中集成的病毒序列的工作流
Conner J Copeland1, Jack W Roddy2, Amelia K Schmidt1
1Division of Biological Sciences, University of Montana, Missoula, MT, 59812, USA.
NAR genomics and bioinformatics
|April 8, 2024
概括
VIBES自动化了细菌基因组中的prophage注释,有助于研究病毒整合及其对细菌健康和毒性的影响. 这种工具增强了我们对菌体及其在微生物生态系统中的作用的理解.
科学领域:
- 微生物学 微生物学
- 生物信息学是一种生物信息学.
- 基因组学就是基因组学.
背景情况:
- 菌体,病毒感染细菌,可以整合到宿主基因组作为prophages.
- 前体会影响细菌的健康状况,充当寄生虫或互利主义者,并可能影响宿主病毒性.
- 细菌基因组测序的进步使得能够详细探索菌的流行率和插入部位.
研究的目的:
- 引入VIBES (细菌基因组中的病毒整合),用于在细菌基因组中实现自动化prophage注释的工作流.
- 通过包括细菌基因和病毒蛋白质注释,为prophage注释提供上下文.
- 为通用序列相似性搜索提供一个多功能工具.
主要方法:
- VIBES是一个Nextflow驱动的工作流程,用于自动化prophage注释.
- 它利用软件依赖性的容器化,确保在整个计算环境中执行一致.
- 工作流执行基于对齐的搜索,并为数据探索生成可视化.
主要成果:
- 在完整的细菌基因组中,VIBES成功地自动化了prophage注释.
- 该工作流通过在1072种*Pseudomonas* spp.中搜索178个Pf基因组来证明. 基因组. 基因组. 这些都是.
- VIBES以分页分隔的格式提供结果,并提供交互式可视化.
结论:
- VIBES是一个高效和用户友好的工具,用于prophage注释.
- 工作流有助于研究菌-宿主相互作用及其进化影响.
- VIBES的设计支持在序列相似性搜索中更广泛的应用.
相关概念视频
02:54Evolutionary Relationships through Genome Comparisons
5.7K
Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
5.7K
03:36Genome Annotation and Assembly
18.8K
The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
18.8K
03:21RNA-seq
9.9K
RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
9.9K