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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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RNA-seq

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RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
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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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RACE - Rapid Amplification of cDNA Ends02:35

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Rapid Amplification of cDNA Ends, or RACE, is one of the most effective methods to obtain a full-length cDNA from an mRNA sequence between a known internal region to the unknown sequence at the 5’ or 3’ end. The unknown region is cloned in the cDNA by a gene-specific primer that binds the known end, and a hybrid primer that attaches a predefined anchor sequence to the unknown end of the cDNA. The sequence in between is amplified by PCR with an anchor primer and a gene-specific...
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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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Genome Annotation and Assembly03:36

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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.
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相关实验视频

Updated: Mar 11, 2026

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
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使用序列和结构信息与树分解重建多个家族的祖先非编码RNA.

Songdi Hu1, Vladimir Reinharz2, Olivier Tremblay-Savard1

  • 1Department of Computer Science, University of Manitoba, Winnipeg, Manitoba, Canada.

Journal of computational biology : a journal of computational molecular cell biology
|March 10, 2026
PubMed
概括
此摘要是机器生成的。

由于结构性保护,重建祖先RNA序列是很困难的. 这项研究引入了一种使用树分解的改进方法,以准确推断祖先非编码RNA (ncRNA) 序列,即使具有多个祖先结构.

关键词:
算法算法是一种算法.这是祖先的推论.这是一个ncRNARNA.人类的基因组学.二级结构是二级结构的二次结构.树的分解 树的分解

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科学领域:

  • 计算生物学 计算生物学
  • 生物信息学是一种生物信息学.
  • 分子进化分子进化

背景情况:

  • 祖先非编码RNA (ncRNA) 序列重建具有挑战性,因为进化压力有利于结构,而不是序列的保存.
  • 以前的方法经常产生比其后代更稳定的祖先序列,从而产生了矛盾.
  • RNA家族可能从具有多个功能和多稳定的结构的祖先分子进化,随后是重复和子专业化.

研究的目的:

  • 为了提高祖先ncRNA序列重建的准确性和减少模糊性.
  • 为了解决假定祖先ncRNAs单一保存结构的方法的局限性.
  • 开发一种能够从相关的ncRNA家族推断出祖先序列的方法,这些序列起源于具有多个功能的单个祖先分子.

主要方法:

  • 开发了一种改进的祖先重建方法,利用树分解算法.
  • 将更多的约束和立场纳入重建过程中.
  • 用一个更现实的能量模型进行序列评估.

主要成果:

  • 在模拟数据集上的祖先序列推理准确度显著改善.
  • 减少了几个数量级推断的最佳祖先序列的数量.
  • 在真实数据集 (RFam 族群 Glm 和 FinP-traJ) 上,新方法推断出较少,与以前的方法相比,结构更适合的祖先序列.

结论:

  • 增强型树分解方法为重建祖先的ncRNA序列提供了更准确,更少含糊的方法.
  • 这种方法有效地处理了祖先的ncRNAs拥有多个功能和结构的场景.
  • 这些发现对了解ncRNA家族的进化历史及其功能多样化有意义.