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相关概念视频

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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Gene Evolution - Fast or Slow?02:05

Gene Evolution - Fast or Slow?

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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...
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Phylogenetic Trees03:21

Phylogenetic Trees

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Phylogenetic trees come in many forms. It matters in which sequence the organisms are arranged from the bottom to the top of the tree, but the branches can rotate at their nodes without altering the information. The lines connecting individual nodes can be straight, angled, or even curved.
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RNA-seq03:21

RNA-seq

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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...
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Taxonomy01:31

Taxonomy

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Taxonomy is the science of defining and naming groups of biological organisms based on shared characteristics. It uses a hierarchy of increasingly inclusive categories with Latin names. The smallest units of taxonomy, species and genus, are used to assign a formal, taxonomic name to each species in a system. This classification system, referred to as binomial nomenclature, was formalized by Carolus Linnaeus in the 18th century.
Hierarchy of Taxonomy
The hierarchy that Carolus Linnaeus first...
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Sanger Sequencing

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DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...
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相关实验视频

Updated: Jun 2, 2025

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
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Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

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phylotypr:用于对DNA序列进行分类的R包.

Patrick D Schloss1

  • 1Department of Microbiology & Immunology, University of Michigan, Ann Arbor, Michigan, USA.

Microbiology resource announcements
|January 14, 2025
PubMed
概括
此摘要是机器生成的。

类型R包使用纯粹的贝叶斯分类来为16S rRNA等基因序列分配分类谱系. 它包括全面的参考数据库,用于准确的微生物社区分析.

关键词:
16S rRNA 是一个16S rRNA.生物信息学是一种生物信息学.这是分类分类的分类.微生物生态学 微生物生态学微生物组是一个微生物组.

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A Practical Guide to Phylogenetics for Nonexperts
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Last Updated: Jun 2, 2025

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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.
  • 计算生物学 计算生物学

背景情况:

  • 微生物群落的准确分类对生态和健康研究至关重要.
  • 16S rRNA基因测序是微生物社区概况的常用方法.
  • 现有的工具需要强大的和最新的分类学数据库来进行可靠的分类.

研究的目的:

  • 引入用于基因序列的分类学分类的类型R包.
  • 为了提供一个用户友好的实现的天真贝叶斯分类器.
  • 提供综合访问多个,精心策划的分类学数据库.

主要方法:

  • 在R编程环境中实现天真贝叶斯分类算法.
  • 开发包含多个分类学数据库的伴侣类型数据包.
  • 使用参考数据库,如核糖体数据库项目 (RDP),SILVA和greengenes.

主要成果:

  • 类型R包为分类16S rRNA和其他基因序列提供了一种有效的方法.
  • 类型数据包提供了一个灵活的资源,包含各种版本的广泛使用的分类学数据库.
  • 组合包为微生物基因组学研究提供了简单而准确的分类学赋值.

结论:

  • 基因类型为需要分类基因序列的研究人员提供了一个有价值的工具.
  • 多个数据库的集成增强了分类的稳定性和适用性.
  • 该方案通过提高分类分辨率来支持微生物生态学和相关领域的进步.