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相关概念视频

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Base complementarity between the three base pairs of mRNA codon and the tRNA anticodon is not a failsafe mechanism. Inaccuracies can range from a single mismatch to no correct base pairing at all. The free energy difference between the correct and nearly correct base pairs can be as small as 3 kcal/ mol. With complementarity being the only proofreading step, the estimated error frequency would be one wrong amino acid in every 100 amino acids incorporated. However, error frequencies observed in...
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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.
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Simultaneous Affinity Enrichment of Two Post-Translational Modifications for Quantification and Site Localization
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梦幻星:平行和空间高效的精确局部对齐.

Evelin Aasna1,2, Simon Gene Gottlieb3, Marcel Ehrhardt3

  • 1Max-Planck-Institut für Molekulare Genetik, Ihnestraße 63-73, 14195, Berlin, Berlin, Germany. aasna@molgen.mpg.de.

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概括
此摘要是机器生成的。

通过克服重复序列的挑战,DREAM-Stellar有效地在大型基因组数据集中找到本地对齐. 这种并行工具显著加快了同类搜索的速度,比现有方法提高了准确性.

关键词:
算法算法是一种算法.生物信息学是一种生物信息学.当地对齐局部对齐平行计算是一种平行计算.

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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:

  • 搜索大型基因组数据集以寻找局部对齐,带来了重大的计算挑战.
  • 基因组数据中的重复序列增加了运行时间成本,并使同质性搜索复杂化.
  • 有效的过器对于减少搜索空间而不会错过重要的匹配至关重要.

研究的目的:

  • 介绍DREAM-Stellar,这是Stellar本地对齐器的更新,并行版本.
  • 开发一个敏感和特定的波器,用于在基因组数据中进行实用的同质性搜索.
  • 将DREAM-Stellar的性能与现有的本地对齐工具进行比较.

主要方法:

  • DREAM-Stellar采用了四个步骤的过程:查询/引用预处理,用于查询分布的数据结构构建,并行计算和结果组合.
  • 使用IBF数据结构和一个新的预过器,以实现高效的本地对齐查询分布.
  • 基于模拟和真实基因组数据评估的性能与其他五个局部对齐器相比.

主要成果:

  • DREAM-Stellar表现出了显著的速度改进,在32个线程上比其前身快900倍.
  • 它可以在几分钟内识别所有双向基因组对齐,在运行时间中与BLAST等工具相比.
  • 像BLAST这样的启发式工具可能会错过重要的本地对齐,或者被不那么重要的匹配所压倒.

结论:

  • DREAM-Stellar是一个实用且快速的工具,用于识别非常长的基因组序列中的局部对齐.
  • 它适合在编辑距离模型下进行同质性搜索.
  • 该软件免费提供给Linux和Mac OS X.