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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 Duplication and Divergence02:37

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The seminal work of Ohno in 1970 popularized the idea of gene duplication and divergence. DNA sequence comparison studies reveal that a large portion of the genes in bacteria, archaebacteria, and eukaryotes was  generated by gene duplication and divergence, indicating its critical role in evolution.
The duplicated copies of the gene are called Paralogs. Paralogs with similar sequences and functions form a gene family. Across several species, a large number of gene families are...
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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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Maxam-Gilbert Sequencing01:05

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In the same year as the discovery of the Sanger sequencing method, another group of scientists, Allan Maxam and Walter Gilbert, demonstrated their chemical-cleavage method for DNA sequencing. The Maxam-Gilbert method relies on using different chemicals that can cleave the DNA sequence at specific sites, the separation of resulting DNA fragments of variable size using electrophoresis, and deciphering the DNA sequence from the resulting gel bands.
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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.
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Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
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基因推断和更灵活的序列聚类使用代-PopPUNK.

Bin Zhao1, John A Lees2,3, Hongjin Wu1

  • 1The Center for Microbes, Development and Health, CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China.

Genome research
|May 30, 2023
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概括

代-PopPUNK通过快速生成跨各种序列身份的灵活,一致的集群来增强细菌谱系推断. 这种方法提高了在公共卫生和临床环境中大规模基因组数据分析的准确性.

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科学领域:

  • 基因组学就是基因组学.
  • 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:

  • 由于广泛的测序应用,细菌基因组数据正在迅速增加.
  • 从大型数据集中准确和高效地进行家谱重建仍然是一个挑战.

研究的目的:

  • 增强PopPUNK方法,提高细菌谱系推断的灵活性和可解释性.
  • 开发一种快速,准确和灵活的聚类方法,并对大型细菌基因组数据集进行基因组分析.

主要方法:

  • 将 PopPUNK 无对齐和无注释方法扩展到代的 PopPUNK.
  • 在一系列序列身份中快速生成多个一致的集群分配.
  • 基于集群分配的部分解决的家谱树的构建.

主要成果:

  • Iterative-PopPUNK在模拟和真实细菌数据集上的聚类和家谱推断方面表现出准确性.
  • 在七种细菌物种中获得了基因组学上一致的结果.
  • 通过使用*Escherichia/Shigella*和*Vibrio parahaemolyticus*的例子,实现了可变的集群分辨率,从族群到序列类型 (ST).

结论:

  • Iterative-PopPUNK提供了一种灵活而准确的方法,用于从大规模基因组数据中重建细菌家谱.
  • 该方法支持用户定义的分辨率级别,用于临床诊断和人口遗传学的各种应用.
  • 代式-PopPUNK算法在"PopPUNK_iterate"程序中实现,以便方便使用.