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相关概念视频

Gene Evolution - Fast or Slow?02:05

Gene Evolution - Fast or Slow?

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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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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 Families01:57

Gene Families

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Gene families consist of groups of genes proposed to have originated from a common ancestor. Typically these arise through events in which a gene or genes are mistakenly duplicated during cell division. Unlike their parent genes (which are subject to selection pressure to maintain function), these gene copies do not need to preserve their sequences and may evolve at a relatively faster rate.
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...
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Genome Annotation and Assembly03:36

Genome Annotation and Assembly

18.7K
The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
18.7K
Exon Recombination02:32

Exon Recombination

3.5K
The evolution of new genes is critical for speciation. Exon recombination, also known as exon shuffling or domain shuffling, is an important means of new gene formation. It is observed across vertebrates, invertebrates, and in some plants such as potatoes and sunflowers. During exon recombination, exons from the same or different genes recombine and produce new exon-intron combinations, which might evolve into new genes. 
Exon shuffling follows “splice frame rules.” Each exon...
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相关实验视频

Updated: May 20, 2025

A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq
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A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq

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使用自行回归生成模型重建祖先蛋白序列.

Matteo De Leonardis1, Andrea Pagnani1,2,3, Pierre Barrat-Charlaix1

  • 1DISAT, Politecnico di Torino, Corso Duca degli Abruzzi 24, Torino 10129, Italy.

Molecular biology and evolution
|March 26, 2025
PubMed
概括

这项研究引入了一种用于祖先序列重建 (ASR) 的新方法,该方法可以解释表观,改进进化模型. 新方法提供了更准确和多样化的祖先蛋白质序列推断.

科学领域:

  • 进化生物学是进化的生物学.
  • 计算生物学是一种计算生物学.
  • 生物物理学的生物物理.

背景情况:

  • 祖先序列重建 (ASR) 有助于理解蛋白质进化.
  • 当前的ASR模型往往忽视了表观性,即突变的上下文依赖性.
  • 生成性蛋白质模型已经进步,学习结构和功能约束.

研究的目的:

  • 为时间依赖的序列进化扩展生成性蛋白质模型,并结合了epistasis.
  • 为了提高准确性和减少推断灭绝的祖先蛋白质序列的偏见.

主要方法:

  • 开发了一个生成模型,能够用epistasis描述随时间推移的序列演变.
  • 将模型应用于使用蛋白质家族和进化树的祖先序列重建.
  • 通过模拟和实验进化数据验证了该方法.

主要成果:

  • 这种新方法的性能优于ASR的现有最先进技术.
  • 这种方法可以采用更广泛的潜在祖先序列样本.
  • 这导致了对祖先蛋白质状态的不那么有偏见的描述.

结论:

关键词:
祖先的序列重建的重建.共同进化的共同进化生成型模型是一种生成型模型.

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  • 将表观性纳入生成模型可以显著提高ASR准确性.
  • 开发的技术为研究蛋白质进化史提供了更全面的工具.
  • 这项工作提高了我们重建和理解过去蛋白质形式和功能的能力.