Jove
Visualize
联系我们
JoVE
x logofacebook logolinkedin logoyoutube logo
关于 JoVE
概览领导团队博客JoVE 帮助中心
作者
出版流程编辑委员会范围与政策同行评审常见问题投稿
图书馆员
用户评价订阅访问资源图书馆顾问委员会常见问题
研究
JoVE JournalMethods CollectionsJoVE Encyclopedia of Experiments存档
教育
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab Manual教师资源中心教师网站
使用条款与条件
隐私政策
政策

相关概念视频

Evolutionary Relationships through Genome Comparisons02:54

Evolutionary 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
Genome Annotation and Assembly03:36

Genome 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
RNA-seq03:21

RNA-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...
9.9K

您也可能阅读

相关文章

通过共同作者、期刊和引用图与本文相关的文章。

排序
Same author

Rational reduction of a sorghum SynCom that preserves growth promotion reveals flavonoid-mediated plant-microbe interactions.

The New phytologist·2026
Same author

Alternatively Spliced Dual-Coding Regions Contribute to the Human Gene Regulatory Program.

bioRxiv : the preprint server for biology·2026
Same author

A prophage-encoded sRNA limits phage infection of adherent-invasive E. coli.

PLoS pathogens·2026
Same author

DIPLOMAT: multi-animal tracking with efficient manual editing.

bioRxiv : the preprint server for biology·2025
Same author

Simpatico: accurate and ultra-fast virtual drug screening with atomic embeddings.

bioRxiv : the preprint server for biology·2025
Same author

NEAR: neural embeddings for amino acid relationships.

Bioinformatics (Oxford, England)·2025

相关实验视频

Updated: Jun 29, 2025

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations
08:03

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

Published on: December 7, 2021

2.1K

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
PubMed
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.

更多相关视频

Combining Analysis of DNA in a Crude Virion Extraction with the Analysis of RNA from Infected Leaves to Discover New Virus Genomes
08:56

Combining Analysis of DNA in a Crude Virion Extraction with the Analysis of RNA from Infected Leaves to Discover New Virus Genomes

Published on: July 27, 2018

11.0K
Isolation and Genome Analysis of Single Virions using 'Single Virus Genomics'
08:31

Isolation and Genome Analysis of Single Virions using 'Single Virus Genomics'

Published on: May 26, 2013

10.9K

相关实验视频

Last Updated: Jun 29, 2025

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations
08:03

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

Published on: December 7, 2021

2.1K
Combining Analysis of DNA in a Crude Virion Extraction with the Analysis of RNA from Infected Leaves to Discover New Virus Genomes
08:56

Combining Analysis of DNA in a Crude Virion Extraction with the Analysis of RNA from Infected Leaves to Discover New Virus Genomes

Published on: July 27, 2018

11.0K
Isolation and Genome Analysis of Single Virions using 'Single Virus Genomics'
08:31

Isolation and Genome Analysis of Single Virions using 'Single Virus Genomics'

Published on: May 26, 2013

10.9K

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.