相关实验视频

Updated: Jul 11, 2025

Phage Phenomics: Physiological Approaches to Characterize Novel Viral Proteins

Phage Phenomics: Physiological Approaches to Characterize Novel Viral Proteins

Published on: June 11, 2015

RVFScan可以预测临床元基因组的毒性因子基因和超毒性

Yue Jiang¹, Xuejiao Hu², Shu Fan¹

¹Department of Bioinformatics, Hugobiotech Co., Ltd., Beijing 100176, China.

Briefings in bioinformatics

|November 6, 2023

概括

一种名为RVFScan的新工具可以直接从元基因组数据中快速识别细菌毒性因子基因 (VFGs),而无需组装. 这有助于诊断诸如Klebsiella pneumoniae之类的高病毒性感染,改善治疗策略.

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:

细菌毒性因子 (VFG) 是致病性的关键,对于诊断和管理感染至关重要.
目前用于从临床元基因组数据中识别VFG的方法通常很慢,缺乏准确性.
快速而精确的VFG检测对于有效的临床治疗和预后至关重要.

研究的目的:

开发一种高效且易于使用的工具,用于从元基因组数据中识别毒性因子基因 (VFGs).
为了实现快速的VFG预测和注释,直接从测序读取,而不需要基因组组装.
评估与现有的VFG预测器相比,开发的工具的性能.

主要方法:

基于Reads的病毒性因素扫描器 (RVFScan) 的开发,这是一个在线工具,集成了VFG数据库和相似性矩阵标准.
使用元基因组数据扫描RVFS的验证,将其性能与基于组装和基于读取的VFG预测器进行比较.
对2425个临床元基因组数据集进行了大规模分析,以评估RVFScan的实用性并确定病原体中的VFG配置文件.

主要成果:

在VFG预测方面,RVFS可以实现高性能,具有97%的灵敏度,98%的特异性和98%的准确性.
对临床数据集的分析揭示了与高病毒性Klebsiella肺炎 (hvKp) 相关的特定VFG配置文件.
在临床队列中,RVFS可以准确地识别hvKp,其灵敏度为90%,特异性为100%,准确度为98.73%.

结论:

RVFScan提供了一种快速,准确和用户友好的方法,用于从不组装的元基因组读取中识别VFG.
该工具有助于在复杂的临床样本中检测高病毒性病原体,如hvKp.
RVFScan具有显著的潜力,可以改善细菌感染的诊断和向治疗,包括由其他高病毒性病原体引起的细菌感染.

关键词:

临床的元基因组学过度病毒的克莱布西拉肺炎.快速检测快速检测迅速检测毒性因子是毒性的因素.

更多相关视频

Purifying the Impure: Sequencing Metagenomes and Metatranscriptomes from Complex Animal-associated Samples

Purifying the Impure: Sequencing Metagenomes and Metatranscriptomes from Complex Animal-associated Samples

Published on: December 22, 2014

Prediction of HIV-1 Coreceptor Usage Tropism by Sequence Analysis using a Genotypic Approach

Prediction of HIV-1 Coreceptor Usage Tropism by Sequence Analysis using a Genotypic Approach

Published on: December 1, 2011

相关概念视频

Rous Sarcoma Virus (RSV) and Cancer

Rous Sarcoma Virus (RSV) and Cancer

Rous Sarcoma virus or RSV was discovered by F. Peyton Rous in the year 1911 as a filterable transmissible agent that could cause tumors in chickens. He won a Nobel Prize for this discovery in 1966. His experiments clearly demonstrated that some cancers could be caused by infectious agents and led to the discovery of many more cancer-causing viruses in animals as well as humans.
RSV is a retrovirus that contains two copies of a plus-strand RNA genome. Its genome consists of four main open...

Viruses of Archaea

Viruses of Archaea

Archaeal viruses play a crucial role in the ecosystems of extremophilic archaea, particularly those belonging to the phyla Euryarchaeota and Crenarchaeota. By shaping host evolution and facilitating gene transfer, these viruses influence microbial communities and contribute to genetic diversity in extreme environments. The archaea they infect thrive in acidic hot springs and hydrothermal vents characterized by high temperatures and low pH. Archaeal viruses exhibit remarkable structural...

Leaky Scanning

Leaky Scanning

During most eukaryotic translation processes, the small 40S ribosome subunit scans an mRNA from its 5' end until it encounters the first start AUG codon. The large 60S ribosomal subunit then joins the smaller one to initiate protein synthesis. The location of the translation initiation is largely determined by the nucleotides near the start codon as there may be multiple translation initiation sites present on the mRNA. Marilyn Kozak discovered that the sequence RCCAUGG (where R...

Viral Mutations

Viral Mutations

A mutation is a change in the sequence of bases of DNA or RNA in a genome. Some mutations occur during replication of the genome due to errors made by the polymerase enzymes that replicate DNA or RNA. Unlike DNA polymerase, RNA polymerase is prone to errors because it is not capable of “proofreading” its work. Viruses with RNA-based genomes, like HIV, therefore accrue mutations faster than viruses with DNA-based genomes. Because mutation and recombination provide the raw material...