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相关概念视频

Genome Annotation and Assembly03:36

Genome Annotation and Assembly

18.9K
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.
18.9K
Next-generation Sequencing03:00

Next-generation Sequencing

91.6K
The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features....
91.6K
S-Cdk Initiates DNA Replication02:38

S-Cdk Initiates DNA Replication

4.7K
The cell cycle is a series of events leading to DNA duplication followed by the division of cell content to form two daughter cells. The cell cycle progresses in four stages—the cell increases in size (gap 1 or G1-phase), duplicates its DNA (synthesis or S-phase), prepares to divide (gap 2 or G2-phase), and divides (mitosis or M-phase).
Two states at the origin of replication
In eukaryotes, the initiation of replication occurs at many sites on the chromosomes, called the origins of...
4.7K
Sanger Sequencing01:57

Sanger Sequencing

755.1K
DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...
755.1K
Genomics02:02

Genomics

36.5K
Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
36.5K
Genomic DNA in Eukaryotes00:58

Genomic DNA in Eukaryotes

47.1K
Eukaryotes have large genomes compared to prokaryotes. To fit their genomes into a cell, eukaryotic DNA is packaged extraordinarily tightly inside the nucleus. To achieve this, DNA is tightly wound around proteins called histones, which are packaged into nucleosomes that are joined by linker DNA and coil into chromatin fibers. Additional fibrous proteins further compact the chromatin, which is recognizable as chromosomes during certain phases of cell division.
47.1K

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相关实验视频

Updated: Jul 25, 2025

Robust DNA Isolation and High-throughput Sequencing Library Construction for Herbarium Specimens
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Robust DNA Isolation and High-throughput Sequencing Library Construction for Herbarium Specimens

Published on: March 8, 2018

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JTK:目标双倍体基因组组装器.

Bansho Masutani1, Yoshihiko Suzuki1, Yuta Suzuki1

  • 1Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan.

Bioinformatics (Oxford, England)
|June 24, 2023
PubMed
概括

JTK是一种新型的双胞胎基因组组装器,使用长读数准确地分阶段单元型,克服了复杂基因组区域的参考方法的局限性. 这项技术可以从单一的测序技术中准确地组装二倍体.

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:

  • 准确的二倍体组合,分离同类染色体,对于理解遗传变异至关重要.
  • 基于参考的分阶段方法与细分重复和结构变化作斗争,导致不可靠的对齐.
  • 像PacBio HiFi这样的现有长期阅读技术需要额外的数据 (ONT或Hi-C) 来完成单 haplotype 阶段化.

研究的目的:

  • 开发一种单一的长时间读取测序技术,能够准确地组装二倍体基因组.
  • 解决目前组装复杂基因组区域的方法的局限性,例如细分重复和结构变异.

主要方法:

  • 介绍了JTK,一个兆基量级的双倍体基因组组装器.
  • 采用千基尺度"块"的随机采样,从长读到相变体并生成单元型.
  • 使用这些块同时捕获单核酸变异 (SNV) 和结构变异 (SV).

主要成果:

  • 在用60倍牛津纳米孔技术 (ONT) 读取的组织相容性复合体 (MHC) 和白细胞受体复合体 (LRC) 区域中,以大约99.9%的准确度实现了完全组装的单元类型.
  • 与日本样本的高覆盖PacBio HiFi + Hi-C数据衍生的组件相比,在LRC地区证明了优越的连续性.
  • 成功组装了难以绘制地图的地区,这些地区以前是基于参考的方法难以处理的.

更多相关视频

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies
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Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies

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Target Cell Pre-enrichment and Whole Genome Amplification for Single Cell Downstream Characterization
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Target Cell Pre-enrichment and Whole Genome Amplification for Single Cell Downstream Characterization

Published on: May 15, 2018

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相关实验视频

Last Updated: Jul 25, 2025

Robust DNA Isolation and High-throughput Sequencing Library Construction for Herbarium Specimens
13:03

Robust DNA Isolation and High-throughput Sequencing Library Construction for Herbarium Specimens

Published on: March 8, 2018

10.7K
Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies
12:08

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies

Published on: August 20, 2021

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Target Cell Pre-enrichment and Whole Genome Amplification for Single Cell Downstream Characterization
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Target Cell Pre-enrichment and Whole Genome Amplification for Single Cell Downstream Characterization

Published on: May 15, 2018

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结论:

  • JTK提供了一个强大的解决方案,用于使用单一的长读测序技术准确的二倍体基因组组装.
  • 这种组装器对于挑战基因组区域特别有效,它补充了现有的基于参考的分阶段方法.
  • JTK准备推进泛基因组学研究,特别是在医学上重要但难以组装的基因组领域.