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

Multi-species Conserved Sequences02:51

Multi-species Conserved Sequences

4.0K
Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale  studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved...
4.0K
Gene Evolution - Fast or Slow?02:05

Gene Evolution - Fast or Slow?

7.2K
The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...
7.2K
Constitutive and Regulated Gene Expression01:27

Constitutive and Regulated Gene Expression

48
Gene expression in prokaryotes is governed by constitutive and regulated systems, allowing cells to balance the production of essential proteins with adaptive responses to environmental changes.Constitutive Gene ExpressionConstitutive, or housekeeping, genes are continuously expressed as they encode proteins vital for fundamental cellular processes. These include enzymes for glycolysis, ribosomal components for protein synthesis, and proteins involved in DNA replication. Their constant...
48
Genome Size and the Evolution of New Genes03:21

Genome Size and the Evolution of New Genes

8.0K
While every living organism has a genome of some kind (be it RNA, or DNA), there is considerable variation in the sizes of these blueprints. One major factor that impacts genome size is whether the organism is prokaryotic or eukaryotic. In prokaryotes, the genome contains little to no non-coding sequence, such that genes are tightly clustered in groups or operons sequentially along the chromosome. Conversely, the genes in eukaryotes are punctuated by long stretches of non-coding sequence.
8.0K
Coordination of Gene Expression Processes in Bacteria01:29

Coordination of Gene Expression Processes in Bacteria

44
The DNA replication, transcription, and translation processes are intricately coupled in bacteria, allowing efficient gene expression and rapid protein synthesis. While this physical and functional coordination is advantageous, it introduces challenges that bacteria overcome through specific regulatory mechanisms.Coupling of Replication, Transcription, and TranslationThe coupling of replication, transcription, and translation is a hallmark of bacterial gene expression. As the replisome unwinds...
44
Reporter Genes02:11

Reporter Genes

11.6K
Reporter genes are a type of protein-coding gene that are often tagged to a gene of interest. Once inside a target cell, reporter genes usually produce visually identifiable characteristics like fluorescence and luminescence when expressed along with the gene of interest. Thus, reporter genes “report” the presence or absence of genes of interest in an organism, determine the gene expression pattern, or track the physical location of a DNA segment or protein in the cell.
11.6K

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

BV-BRC: a unified bacterial and viral bioinformatics resource with expanded functionality and AI integration.

Nucleic acids research·2025
Same author

Using intrahost single nucleotide variant data to predict SARS-CoV-2 detection cycle threshold values.

PloS one·2024
Same author

Comparative Genomic Analysis of Bacterial Data in BV-BRC: An Example Exploring Antimicrobial Resistance.

Methods in molecular biology (Clifton, N.J.)·2024
Same author

Engineering of increased L-Threonine production in bacteria by combinatorial cloning and machine learning.

Metabolic engineering communications·2023
Same author

Efficient Adeno-associated Virus-mediated Transgenesis in Alveolar Stem Cells and Associated Niches.

American journal of respiratory cell and molecular biology·2023
Same author

A Global Survey of Hypervirulent <i>Aeromonas hydrophila</i> (vAh) Identified vAh Strains in the Lower Mekong River Basin and Diverse Opportunistic Pathogens from Farmed Fish and Other Environmental Sources.

Microbiology spectrum·2023

相关实验视频

Updated: Jul 26, 2025

Mapping Bacterial Functional Networks and Pathways in Escherichia Coli using Synthetic Genetic Arrays
14:06

Mapping Bacterial Functional Networks and Pathways in Escherichia Coli using Synthetic Genetic Arrays

Published on: November 12, 2012

46.5K

使用保存的基因预测大肠杆菌中的可变基因含量.

Marcus Nguyen1,2, Zachary Elmore3, Clay Ihle3

  • 1Data Science and Learning Division, Argonne National Laboratory , Lemont, Illinois, USA.

mSystems
|June 14, 2023
PubMed
概括

机器学习准确地预测了Escherichia coli基因组中的可变基因含量,使用保存的基因k-mers. 该框架有助于对生物信息学任务进行基因组分析和风险评估.

关键词:
抗微生物耐药性 抗微生物耐药性细菌病毒性的毒性.横向基因转移是指水平基因转移.机器学习是机器学习.人类的基因组学.

更多相关视频

Determination of the Optimal Chromosomal Locations for a DNA Element in Escherichia coli Using a Novel Transposon-mediated Approach
11:12

Determination of the Optimal Chromosomal Locations for a DNA Element in Escherichia coli Using a Novel Transposon-mediated Approach

Published on: September 11, 2017

7.6K
Characterization of a Pathogenic Escherichia coli Strain Derived from Oreochromis spp. Farms Using Whole-Genome Sequencing
09:44

Characterization of a Pathogenic Escherichia coli Strain Derived from Oreochromis spp. Farms Using Whole-Genome Sequencing

Published on: December 23, 2022

2.2K

相关实验视频

Last Updated: Jul 26, 2025

Mapping Bacterial Functional Networks and Pathways in Escherichia Coli using Synthetic Genetic Arrays
14:06

Mapping Bacterial Functional Networks and Pathways in Escherichia Coli using Synthetic Genetic Arrays

Published on: November 12, 2012

46.5K
Determination of the Optimal Chromosomal Locations for a DNA Element in Escherichia coli Using a Novel Transposon-mediated Approach
11:12

Determination of the Optimal Chromosomal Locations for a DNA Element in Escherichia coli Using a Novel Transposon-mediated Approach

Published on: September 11, 2017

7.6K
Characterization of a Pathogenic Escherichia coli Strain Derived from Oreochromis spp. Farms Using Whole-Genome Sequencing
09:44

Characterization of a Pathogenic Escherichia coli Strain Derived from Oreochromis spp. Farms Using Whole-Genome Sequencing

Published on: December 23, 2022

2.2K

科学领域:

  • 基因组学和生物信息学
  • 计算生物学 计算生物学
  • 机器学习在生物学中的应用

背景情况:

  • 预测编码蛋白质的基因含量对于分析不完整或组装的基因组至关重要.
  • 准确的基因含量预测支持各种生物信息学任务,包括基因组质量评估和风险评估.

研究的目的:

  • 开发和验证机器学习分类器,用于预测大肠杆菌基因组中的可变基因含量.
  • 证明使用保存基因中的核酸k-mers作为基因含量预测特征的实用性.

主要方法:

  • 构建了3,259个极端梯度增强分类器,以预测大肠杆菌基因组中蛋白质家族的存在/缺席.
  • 从100个保存的基因中利用核酸k-mers作为输入特征.
  • 定义了使用蛋白质家族和专注于基因在10%-90%的基因组中存在的基因.

主要成果:

  • 在所有分类器中获得0.944的高平均宏观F1得分.
  • 证明了对标注差的蛋白质 (F1 = 0.902) 和与水平基因转移相关的基因 (F1s从0.824到0.895不等) 的准确预测.
  • 在来自环境来源的E. coli基因组 (平均F1分数为0.880) 的多样化的持久集上验证了模型性能.

结论:

  • 已经建立了一个强大的框架,用于使用有限序列数据预测可变基因含量.
  • 开发的模型是准确的,稳定在不同的大肠杆菌菌株,并可扩展到不同的基因组数据集.
  • 这种方法为增强微生物基因组学中的基因组分析和风险评估提供了有价值的策略.