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相关概念视频

Maxam-Gilbert Sequencing01:05

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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
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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...
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Methodology for Accurate Detection of Mitochondrial DNA Methylation
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使用PacBio循环共识测序检测DNA5甲基氨酸和甲基化分相.

Peng Ni1,2,3, Fan Nie1,2,3, Zeyu Zhong1,3

  • 1School of Computer Science and Engineering, Central South University, Changsha, 410083, China.

Nature communications
|July 8, 2023
PubMed
概括

我们开发了ccsmeth,这是一个深度学习工具,用于使用PacBio循环共识测序 (CCS) 读取精确的DNA5甲基细胞素 (5mCpC) 检测. 这种方法增强了重复区域的甲基化分析,并提供了对单 haplotype 意识的见解.

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科学领域:

  • 基因组学就是基因组学.
  • 表观遗传学 在表观遗传学中,表观遗传学是指表观遗传学.
  • 生物信息学是一种生物信息学.

背景情况:

  • 像PacBio CCS和纳米孔测序等长期读取的测序技术显示出检测DNA5-甲基细胞素 (5mCpG) 的前景.
  • 目前用于5mCpG检测的PacBio CCS方法缺乏准确性和稳定性,特别是在复杂的基因组区域.

研究的目的:

  • 开发一种新的深度学习方法,ccsmeth,用于使用PacBio CCS读取的DNA5mCpG的准确和强大的检测.
  • 从CCS数据创建一个Nextflow管道,ccsmethphase,用于从CCS数据中对哈普类型有意识的甲基化检测.

主要方法:

  • 使用PacBio CCS训练的ccsmeth从聚合酶链反应处理和M.SssI-甲基转移酶处理的人类DNA中读取.
  • 评估了ccsmeth在单分子分辨率下检测5mCpG的性能,使用长时间的CCS读数 (≥10 Kb).
  • 开发了ccsmethphase管道用于表型感知甲基化分析,并使用中国家族三组进行了验证.

主要成果:

  • 对于单分子5mCpG检测,ccsmeth实现了0.90准确度和0.97曲线下的面积.
  • 全基因组站点级分析显示>0.90与二硫酸盐和纳米孔序列的相关性,仅使用10×CCS读数.
  • ccsmethphase成功检测出对单 haplotype 有意识的甲基化模式.

结论:

  • ccsmeth提供了一种强大而准确的深度学习方法,用于使用PacBio CCS长读数检测DNA 5mCpG.
  • ccsmethphase能够进行敏感的单元型感知甲基化分析,从而推进表观遗传学研究.
  • 这些工具为DNA甲基化分析提供了显著的改进,特别是在具有挑战性的基因组领域.