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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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Maxam-Gilbert Sequencing01:05

Maxam-Gilbert Sequencing

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In the same year as the discovery of the Sanger sequencing method, another group of scientists, Allan Maxam and Walter Gilbert, demonstrated their chemical-cleavage method for DNA sequencing. The Maxam-Gilbert method relies on using different chemicals that can cleave the DNA sequence at specific sites, the separation of resulting DNA fragments of variable size using electrophoresis, and deciphering the DNA sequence from the resulting gel bands.
Challenges of the Maxam-Gilbert Method
The...
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DNA Base Pairing02:27

DNA Base Pairing

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Erwin Chargaff’s rules on DNA equivalence paved the way for the discovery of base pairing in DNA. Chargaff’s rules state that in a double-stranded DNA molecule,
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Combinatorial Gene Control02:33

Combinatorial Gene Control

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Combinatorial gene control is the synergistic action of several transcriptional factors to regulate the expression of a single gene. The absence of one or more of these factors may lead to a significant difference in the level of gene expression or repression.
The expression of more than 30,000 genes is controlled by approximately 2000-3000 transcription factors. This is possible because a single transcription factor can recognize more than one regulatory sequence. The specificity in gene...
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Gene Duplication and Divergence02:37

Gene Duplication and Divergence

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The seminal work of Ohno in 1970 popularized the idea of gene duplication and divergence. DNA sequence comparison studies reveal that a large portion of the genes in bacteria, archaebacteria, and eukaryotes was  generated by gene duplication and divergence, indicating its critical role in evolution.
The duplicated copies of the gene are called Paralogs. Paralogs with similar sequences and functions form a gene family. Across several species, a large number of gene families are...
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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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Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations
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对于循环泛基组图的间隙敏感的直角链接算法

Ghanshyam Chandra1, Chirag Jain1

  • 1Department of Computational and Data Sciences, Indian Institute of Science Bengaluru, India.

Journal of computational biology : a journal of computational molecular cell biology
|October 30, 2023
PubMed
概括

泛基因组图为物种提供了一个紧的基因组参考. 本研究引入了序列对图对齐的新算法,提高了基因组研究的准确性和效率.

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.

背景情况:

  • 泛基因组图提供了一种物种内的多个基因组的紧表示,对于先进的基因组研究至关重要.
  • 将序列与泛基因组图进行对齐对于基于泛基因组的再测序至关重要.

研究的目的:

  • 开发高效准确的序列到图的对齐算法,并结合各种差距成本函数.
  • 解决不考虑差距成本的现有框架的局限性.

主要方法:

  • 开发了用于序列到图形链接的新型问题表述.
  • 设计了可证明良好的链接算法,支持各种差距成本函数.
  • 使用了稀疏的动态编程框架,利用非循环泛列组图的路径覆盖属性.

主要成果:

  • 实现了98.7%的精度在绘制模拟长读到一个95-haplotype人类基因组图.
  • 只有不到2%的读数没有被映射出来,这表明了高效率.
  • 与现有对齐器相比,经验证明了优越的性能.

结论:

  • 新型链接算法有效地处理各种差距成本函数用于序列对图对齐.
  • 开发的方法显著提高了基于泛基因组的再测序的实际有效性.
关键词:
最低路径覆盖面的最低路径覆盖面.顺序对齐的顺序对齐.稀少的动态编程是稀少的.一个变化图的变化图.

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A Novel Bayesian Change-point Algorithm for Genome-wide Analysis of Diverse ChIPseq Data Types
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  • 这项工作推进了泛基因组图的实用性,作为基因组研究中的参考.