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相关概念视频

Next-generation Sequencing03:00

Next-generation Sequencing

87.5K
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....
87.5K
RNA-seq03:21

RNA-seq

9.8K
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...
9.8K
Sanger Sequencing01:57

Sanger Sequencing

752.9K
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...
752.9K
Conservative Site-specific Recombination and Phase Variation02:53

Conservative Site-specific Recombination and Phase Variation

5.9K
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...
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Ribosome Profiling02:24

Ribosome Profiling

3.5K
Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...
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相关实验视频

Updated: Jun 6, 2025

Rare Event Detection Using Error-corrected DNA and RNA Sequencing
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Rare Event Detection Using Error-corrected DNA and RNA Sequencing

Published on: August 3, 2018

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Repun:一个准确的小变体表示统一方法,用于多个测序平台.

Zhenxian Zheng1, Yingxuan Ren1, Lei Chen1

  • 1Department of Computer Science, The University of Hong Kong, Pok Fu Lam Road, Hong Kong, 999077, China.

Briefings in bioinformatics
|November 25, 2024
PubMed
概括
此摘要是机器生成的。

在变量调用之前,Repun统一了变量表示在测序数据中的变量表示,提高了准确性,并使更好的深度学习模型训练成为可能. 这种分类型感知算法在多个测序平台上实现了高精度和回忆.

关键词:
哈普洛型的比较和对比多平台测序多平台测序代表性 统一 统一 代表性变量调用变量调用变体表示的变体表示.

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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:

  • 统一的变种表示对于准确的下游基因组分析至关重要.
  • 当前的方法经常统一调用后的变体,错过了早期质量评估的机会.
  • 变体表示的差异源于不同的测序平台和条件.

研究的目的:

  • 开发一个新的算法,Repun,用于协调变量和对齐表示.
  • 为了实现变异统一,需要改进数据质量和模型培训.
  • 为了应对统一期间处理众多变体候选人的挑战.

主要方法:

  • 开发了Repun,这是一个对哈普罗类型有意识的变体对齐统一算法.
  • 杆化分阶段来匹配变体和对齐单元型.
  • 利用带有读取证据的哈普洛类型来优化统一过程.

主要成果:

  • Repun实现了>99.99%的精度和>99.5%的回忆.
  • 在牛津纳米孔技术,太平洋生物科学和Illumina平台上得到验证.
  • 在"瓶中的基因组"联盟样本上证明有效性.

结论:

  • 雷邦为变种对齐统一提供了一个强大的解决方案.
  • 早期统一增强下游分析和深度学习模型培训.
  • 开源的Repun算法支持多种不同的测序数据类型.