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相关概念视频

Viral Mutations00:36

Viral Mutations

32.0K
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...
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Viral Structure00:56

Viral Structure

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Viruses are extraordinarily diverse in shape and size, but they all have several structural features in common. All viruses have a core that contains a DNA- or RNA-based genome. The core is surrounded by a protective coat of proteins called the capsid. The capsid is composed of subunits called capsomeres. The capsid and genome-containing core are together known as the nucleocapsid.
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Viral Recombination00:57

Viral Recombination

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Cells are sometimes infected by more than one virus at once. When two viruses disassemble to expose their genomes for replication in the same cell, similar regions of their genomes can pair together and exchange sequences in a process called recombination. Alternatively, viruses with segmented genomes can swap segments in a process called reassortment.
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Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

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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...
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Classification of Leukocytes01:30

Classification of Leukocytes

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Leukocytes are classified into two groups based on the presence or absence of cytoplasmic granules. Granular leukocytes, which contain granules, belong to the myeloid lineage and are divided into three subtypes: neutrophils, eosinophils, and basophils. These cells are roughly spherical and characterized by the granules in their cytoplasm.
Neutrophils are the most abundant type of granular leukocytes, comprising 50-70% of all leukocytes. They feature small, evenly distributed granules and a...
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Leaky Scanning02:28

Leaky Scanning

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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...
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相关实验视频

Updated: May 11, 2025

Unbiased Deep Sequencing of RNA Viruses from Clinical Samples
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Unbiased Deep Sequencing of RNA Viruses from Clinical Samples

Published on: July 2, 2016

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在规模上进行无对齐的病毒序列分类.

Daniel J van Zyl1,2, Marcel Dunaiski3, Houriiyah Tegally4

  • 1Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa. danielvanzyl@sun.ac.za.

BMC genomics
|April 18, 2025
PubMed
概括
此摘要是机器生成的。

无对齐方法为病毒序列分类提供了一个可扩展和快速的替代方案. 这些技术在大型数据集上实现了高精度,优于传统的基于对齐的方法.

关键词:
没有对齐的自由对齐.生物序列的生物序列.功能提取 功能提取机器学习 机器学习病毒的分类 病毒的分类

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Isolation of Fidelity Variants of RNA Viruses and Characterization of Virus Mutation Frequency

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A Virtual Machine Platform for Non-Computer Professionals for Using Deep Learning to Classify Biological Sequences of Metagenomic Data
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相关实验视频

Last Updated: May 11, 2025

Unbiased Deep Sequencing of RNA Viruses from Clinical Samples
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Unbiased Deep Sequencing of RNA Viruses from Clinical Samples

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Isolation of Fidelity Variants of RNA Viruses and Characterization of Virus Mutation Frequency
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Isolation of Fidelity Variants of RNA Viruses and Characterization of Virus Mutation Frequency

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A Virtual Machine Platform for Non-Computer Professionals for Using Deep Learning to Classify Biological Sequences of Metagenomic Data
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A Virtual Machine Platform for Non-Computer Professionals for Using Deep Learning to Classify Biological Sequences of Metagenomic Data

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科学领域:

  • 生物信息学是一种生物信息学.
  • 计算生物学 计算生物学
  • 基因组学就是基因组学.

背景情况:

  • 下一代测序 (NGS) 产生了大量的核酸数据,需要高效的测序比较工具.
  • 传统的基于对齐的方法 (例如,BLAST) 在大规模数据集的可扩展性方面扎.
  • 无对齐 (AF) 方法为序列分析提供了一个有希望的,计算效率高的替代方案.

研究的目的:

  • 评估AF方法的大规模病毒序列分类的有效性.
  • 识别 AF 技术,以平衡精度和计算效率.
  • 在各种病毒数据集中评估AF方法的性能.

主要方法:

  • 使用六种已建立的AF技术,从病毒基因组中生成特征向量.
  • 随机森林分类器使用这些特征向量进行训练.
  • 模型在广泛的SARS-CoV-2,登革热和HIV序列数据集上得到验证.

主要成果:

  • AF分类器的准确性很高:SARS-CoV-2的97.8%,登革热的99.8%,HIV的89.1%.
  • 基于文字的AF方法有效地表示病毒序列,即使具有高维度.
  • 在不同的病毒基因组数据集中展示了强度和可扩展性.

结论:

  • AF方法为病毒序列分类提供了实用和有效的解决方案.
  • 这些技术比基于对齐的方法提供了显著的速度优势.
  • AF方法允许使用有限的计算资源进行序列分类.