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相关概念视频

Protein Families02:47

Protein Families

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Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism.   Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members.   If these new proteins contain similar amino acids in key...
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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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Convergent Evolution01:54

Convergent Evolution

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Evolution shapes the features of organisms over time, ensuring that they are suited for the environments in which they live. Sometimes, selection pressure leads to the rise of similar but unrelated adaptations in organisms with no recent common ancestors, a process known as convergent evolution.
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Structural Protein Function

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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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相关实验视频

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A Protocol for Computer-Based Protein Structure and Function Prediction
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A Protocol for Computer-Based Protein Structure and Function Prediction

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评估序列和结构相似度指标,用于预测共享的对等函数.

Olivier Dennler1,2,3, Colm J Ryan1,2,3

  • 1School of Medicine, University College Dublin, Dublin 4, D04 V1W8, Ireland.

NAR genomics and bioinformatics
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概括
此摘要是机器生成的。

新的蛋白质相似度指标,包括结构和语言模型嵌入,比单独的序列身份更好地预测基因对比函数. 结合这些新的方法可以提高功能预测的准确性.

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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:

  • 基因重复是新基因进化的主要驱动因素,产生常常保留类似功能的类似基因.
  • 蛋白序列标识是功能相似性的常见代理,有助于预测对象之间的共享功能.
  • 新兴的蛋白质表示,如蛋白质语言模型 (PLM) 嵌入和AlphaFold预测结构,为评估功能相似性提供了新的途径.

研究的目的:

  • 为了评估超越序列身份的替代蛋白质相似度指标,以预测共享的对比功能.
  • 为了确定结构性或基于PLM的相似度量是否可以超越或补充序列身份.
  • 为了研究上下文特征的影响,如同类学,预测共享的方程函数.

主要方法:

  • 使用两种物种 (酵母,人类) 的各种相似度量 (序列相同性,PLM嵌入,结构相似性) 的比较.
  • 基于蛋白质-蛋白质相互作用和合成致命性的共享功能评估.
  • 整合的上下文特征代表跨物种和物种内部的同质性.

主要成果:

  • 其他相似度指标,包括基于结构和PLM的方法,在预测共享的对应函数方面表现出了很好的前景.
  • 这些新的指标并没有冗余的序列标识,并且在结合时可以改善预测.
  • 整合上下文同类特征显著提高了预测共享paralog功能的准确性.

结论:

  • 替代蛋白质相似度指标捕捉了不仅仅由序列身份表示的功能方面.
  • 将序列标识与结构,PLM和上下文同类特征相结合,为预测对应函数提供了更全面的方法.
  • 这些发现表明,通过比较基因组学,可以改进理解基因功能和进化过程的方法.