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相关概念视频

Phylogeny01:23

Phylogeny

44.2K
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.
44.2K
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

5.8K
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...
5.8K
Multi-species Conserved Sequences02:51

Multi-species Conserved Sequences

3.9K
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
Conservative Site-specific Recombination and Phase Variation02:53

Conservative Site-specific Recombination and Phase Variation

6.0K
Because the DNA segments are cut and reorganized in a direction-specific manner, site-specific recombination has emerged as an efficient genetic engineering technique. Flippase and Cyclization recombinases or Flp and Cre, respectively, are two members of the tyrosine recombinase family derived from bacteriophages, that are used to mediate site-specific DNA insertions, deletions, and targeted expression of proteins in mammalian cell lines.
The recognition sites for Cre recombinase called LoxP...
6.0K
Genome Copying Errors02:46

Genome Copying Errors

4.2K
DNA replication is a well-evolved process that copies millions of base pairs with high fidelity during each cell division. Occasionally a wrong base or a long stretch of wrong bases may get added to the daughter strands. If the errors are left unchecked, cells might accumulate several mutations that might endanger their  survival. Therefore, the copying errors are checked and repaired at three levels.
4.2K
Synteny and Evolution02:31

Synteny and Evolution

3.3K
John H. Renwick first coined the term “synteny” in 1971, which refers to the genes present on the same chromosomes, even if they are not genetically linked. The species with common ancestry tend to show conserved syntenic regions. Therefore, the concept of synteny is nowadays used to describe the evolutionary relationship between species.
Around 80 million years ago, the human and mice lineages diverged from the common ancestor. During the course of evolution, the ancestral...
3.3K

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相关实验视频

Updated: Jul 9, 2025

A Practical Guide to Phylogenetics for Nonexperts
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A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

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康尼弗 (CONIPHER):一个计算框架,用于具有错误纠正的可扩展的家族遗传重建.

Kristiana Grigoriadis1,2,3, Ariana Huebner1,2,3, Abigail Bunkum1,4,5

  • 1Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.

Nature protocols
|November 28, 2023
PubMed
概括
此摘要是机器生成的。

康尼弗通过纠正序列错误和副本数量改变,准确地重建瘤演变. 这种计算框架从DNA测序数据中改进了癌症亚克隆架构的遗传学分析.

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Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
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相关实验视频

Last Updated: Jul 9, 2025

A Practical Guide to Phylogenetics for Nonexperts
12:00

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

35.4K
Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
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Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

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An Integrated Approach for Microprotein Identification and Sequence Analysis
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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
  • 癌症研究 癌症研究

背景情况:

  • 瘤内部的异质性推动了癌症的演变.
  • 从DNA测序中准确推断瘤亚克隆结构和进化史,由于文物和错误而具有挑战性.
  • 现有的方法难以应对拷贝数的变化和突变损失,这会影响遗传学重建.

研究的目的:

  • 介绍CONIPHER,用于准确推断瘤亚克隆结构和系遗传关系的计算框架.
  • 为了应对瘤进化史重建的挑战,从多样本DNA测序数据重建.
  • 为分析复杂的癌症基因组提供强大的工具.

主要方法:

  • 开发了CONIPHER (在植物遗传评估和重建中纠正噪声) 计算框架.
  • 对复制数的变化和基因组分析中的突变错误进行核算.
  • 适用于多样本瘤测序数据,包括全外体测序和初级转移病例.

主要成果:

  • 康尼弗精确地推断出亚克隆结构和家族遗传关系.
  • 该框架成功地被应用到从TRACERx421数据集中重建瘤系谱.
  • 在模拟数据上,CONIPHER的性能优于类似的方法,并可扩展到大型数据集.

结论:

  • 康尼弗提供了一种准确而强大的方法来重建瘤进化史.
  • 该框架可用于跨不同技术的大规模测序数据集的自动化基因分析.
  • 对于具有基本生物信息学和脚本知识的用户来说,CONIPHER是可访问的.