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相关概念视频

Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

5.7K
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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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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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...
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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...
3.9K
Conserved Binding Sites01:49

Conserved Binding Sites

4.2K
Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...
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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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相关实验视频

Updated: Jun 24, 2025

Demonstration of the Sequence Alignment to Predict Across Species Susceptibility Tool for Rapid Assessment of Protein Conservation
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Demonstration of the Sequence Alignment to Predict Across Species Susceptibility Tool for Rapid Assessment of Protein Conservation

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COATi:蛋白质编码序列的统计对照对齐.

Juan José García Mesa1,2, Ziqi Zhu1,3, Reed A Cartwright1,3

  • 1The Biodesign Institute, Arizona State University, Tempe, AZ, USA.

Molecular biology and evolution
|June 13, 2024
PubMed
概括
此摘要是机器生成的。

COATi是一种新的编码子感知序列对齐器,可以准确地处理编码子内的生物序列文物和内置. 这可以改善基因组学和进化研究的数据分析.

关键词:
编码序列的编码序列.码头模型的模型在Indel的阶段.双向对齐的对齐是双向对齐的统计对齐统计对齐

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相关实验视频

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Demonstration of the Sequence Alignment to Predict Across Species Susceptibility Tool for Rapid Assessment of Protein Conservation
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An Integrated Approach for Microprotein Identification and Sequence Analysis
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科学领域:

  • 生物信息学是一种生物信息学.
  • 计算生物学 计算生物学
  • 基因组学就是基因组学.

背景情况:

  • 序列对齐对于生物信息学分析至关重要,例如遗传学推断和基因注释.
  • 测序文物和组装错误 (例如,移,过早停止编码子) 可以导致基因组研究中的错误结论.
  • 现有的对齐器经常错误地假设插入/删除 (indels) 仅发生在子之间,而不是它们内部,导致次优对齐.

研究的目的:

  • 介绍COATi,一个统计,编码子意识的双向对齐器.
  • 解决当前调整器在处理生物内置和测序文物方面的局限性.
  • 提高精度,减少数据丢失在序列对齐.

主要方法:

  • 开发了COATi,这是一个统计,编码子意识的双向序列对齐器.
  • 实施了复杂的插入-删除模型,能够处理代码体内和代码体之间的生物内置.
  • 在人类和大猩猩的正统蛋白质编码序列以及基准对齐上测试了COATi.

主要成果:

  • COATi 准确地推断出 codon 内部和 codon 之间发生的 indels.
  • 对人类-大猩猩序列的分析显示,41%的indels发生在codons之间.
  • 在基准数据集的质量和准确性指标上,COATi表现优于受欢迎的对齐程序.

结论:

  • COATi有效地处理测序文物和复杂的indel模式,提高对齐准确度.
  • 调整器减少了丢弃数据的需要,增强了下游比较和功能基因组分析.
  • 在生物信息学中,COATi代表了精确序列对齐的重大进步.