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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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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...
7.0K
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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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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Multi-species Conserved Sequences02:51

Multi-species Conserved Sequences

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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...
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Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

10.8K
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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Eukaryotic Evolution01:24

Eukaryotic Evolution

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The endosymbiont theory is the most widely accepted theory of eukaryotic evolution; however, its progression is still somewhat debated. According to the nucleus-first hypothesis, the ancestral prokaryote first evolved a membrane to enclose DNA and form the nucleus. Conversely, the mitochondria-first hypothesis suggests that the nucleus was formed after endosymbiosis of mitochondria.
Contrary to the endosymbiont theory, the eukaryote-first hypothesis proposes that the simpler prokaryotic and...
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相关实验视频

Updated: May 30, 2025

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

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MyESL:分子进化和遗传学分析中的稀疏学习

Maxwell Sanderford1, Sudip Sharma1,2, Glen Stecher1

  • 1Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA 19122, USA.

ArXiv
|January 27, 2025
PubMed
概括

进化稀疏学习 (ESL) 模型使用 LASSO.使用基因组特征变异. MyESL软件有效地分析大型基因组数据集以获得进化见解,优于现有的工具.

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A Practical Guide to Phylogenetics for Nonexperts
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相关实验视频

Last Updated: May 30, 2025

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科学领域:

  • 基因组学就是基因组学.
  • 计算生物学 计算生物学
  • 机器学习 机器学习

背景情况:

  • 进化稀疏学习 (ESL) 应用监督机器学习,特别是 LASSO,以建模假设和基因组特征变异之间的关系.
  • 现有的稀疏组 LASSO 软件与全基因组序列数据的规模作斗争,需要专门的工具.

研究的目的:

  • 推出MyESL,这是一个开源软件包,旨在对大型基因组数据集进行高效和灵活的ESL分析.
  • 为进化基因组学提供预处理工具,灵活的LASSO模型构建和结果后处理.

主要方法:

  • MyESL使用C++核心用于计算密集型模型构建 (带或不带组稀疏性) 和Python用于前/后处理.
  • 输入数据,包括二进制响应或家族遗传树和序列对齐,被转换成适合LASSO分析的格式.
  • 该软件处理连续和二进制特征,将序列对齐转换为二进制一热编码矩阵.

主要成果:

  • 在标准桌面计算机上,MyESL成功地快速高效地构建进化模型.
  • 经验性基因组规模数据集分析表明MyESL的能力在其他软件包由于资源限制而失败的地方.
  • 该软件生成用户友好的文本和图形输出,用于下游解释.

结论:

  • MyESL解决了ESL现有软件在大规模基因组数据上的局限性.
  • 它为进化和功能基因组学研究提供了一个计算效率高且易于使用的解决方案.
  • MyESL可用于Linux,Windows和macOS,促进整合到各种生物信息管道中.