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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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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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Phylogeny01:23

Phylogeny

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Phylogeny is concerned with the evolutionary diversification of organisms or groups of organisms. A group of organisms with a name is called a taxon (singular). Taxa (plural) can span different levels of the evolutionary hierarchy. For instance, the group containing all birds is a taxon (comprising the class Aves), and the group of all species of daisies (the genus Bellis) is a taxon. Phylogenies can likewise include just one genus (i.e., depict species relationships) or span an entire kingdom.
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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.
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Gene Duplication and Divergence02:37

Gene Duplication and Divergence

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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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Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

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Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...
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相关实验视频

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Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
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通过多多波嵌入的多多纳基与多多纳基的差异化基因学.

Matthew Macaulay1, Mathieu Fourment1

  • 1Australian Institute for Microbiology & Infection, University of Technology Sydney, Ultimo, NSW 2007, Australia.

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概括
此摘要是机器生成的。

我们介绍软NJ,一个可差分的方法来优化家族遗传树. 这种方法使得基于梯度的方法能够在超标空间中进行高效的基因推理推理,从而推进计算基因学.

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科学领域:

  • 计算型的遗传学学.
  • 机器学习 机器学习
  • 生物信息学是一种生物信息学.

背景情况:

  • 在高维离散空间中优化家族遗传树是计算上具有挑战性的.
  • 超标嵌入式为树提供高效的连续空间编码.
  • 不同化的树解码器是优化类遗传概率所必需的.

研究的目的:

  • 为了介绍软NJ,一个微分版本的邻居连接算法.
  • 为了使基于梯度的优化能够直接在族系树的空间上进行.
  • 应用可微分树嵌入用于变异贝叶斯系遗传学.

主要方法:

  • 开发软NJ,一个可差分类树解码器用于遗传学分析.
  • 利用过度嵌入式嵌入,以在连续空间中高效地表示树.
  • 通过优化嵌入分布来执行变量贝叶斯推理.

主要成果:

  • 证明了可微分优化对于最大概率推理的潜力.
  • 在与最先进的方法对比的八个基准数据集上评估软NJ的性能.
  • 通过树嵌入展示软NJ作为一种强大而高效的方法,通过树嵌入,尽管潜在的本地最佳.

结论:

  • 软-NJ促进了基于梯度的优化在遗传树的空间.
  • 超标嵌入与软NJ相结合,提供了一个参数效率高的基因组学方法.
  • 软件包Dodonaphy实现软-NJ,使其可用于研究.