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相关概念视频

RACE - Rapid Amplification of cDNA Ends02:35

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Rapid Amplification of cDNA Ends, or RACE, is one of the most effective methods to obtain a full-length cDNA from an mRNA sequence between a known internal region to the unknown sequence at the 5’ or 3’ end. The unknown region is cloned in the cDNA by a gene-specific primer that binds the known end, and a hybrid primer that attaches a predefined anchor sequence to the unknown end of the cDNA. The sequence in between is amplified by PCR with an anchor primer and a gene-specific...
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rCRUX:用于生成R中的元编码参考库的快速和多功能工具.

Emily E Curd1, Luna Gal2,3, Ramon Gallego4

  • 1Vermont Biomedical Research Network, University of Vermont, VT, USA.

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概括
此摘要是机器生成的。

该rCRUX R包生成了用于metabarcoding的全面DNA条形码参考库. 它克服了现有工具的局限性,通过使用序列同质性和原始相容性来准确分类.

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科学领域:

  • 生物信息学是一种生物信息学.
  • 分子生态学分子生态学
  • 基因组学就是基因组学.

背景情况:

  • 精确的DNA序列分类对生物多样性监测和研究至关重要.
  • 由于序列数据的快速增长以及对不同基因区域和种类的需求,现有的参考条形码数据库面临策划方面的挑战.
  • 需要用户友好的计算工具来生成自定义的元编码参考库.

研究的目的:

  • 介绍一下rCRUX,一个旨在自动生成全面,精心策划的元编码参考库的R包.
  • 提供一个依赖于序列同质性和PCR原料兼容性的工具,避免元数据限制.
  • 为各种DNA测序应用提供准确的分类学分类.

主要方法:

  • rCRUX模拟in silico PCR以根据用户定义的原始序列识别种子安普利康.
  • 与NCBI nt数据库相对应的代BLAST搜索使用分层随机抽样进行.
  • 数据库被取消复制和清理,以确保分类学准确性和最低共同协议.

主要成果:

  • 与现有的工具 (CRABS,MetaCurator,RESCRIPt,ecoPCR) 相比,rCRUX对于几个loci (MiFish 12S,Taberlet trnl,真菌ITS,Leray CO1) 产生了更全面的参考数据库.
  • 该软件包成功生成了24个参考数据库,用于20个metabarcoding loci,包括那些缺乏专门策划工作的数据库.
  • 证明了rCRUX在为各种分类组和基因区域创建定制参考库方面的实用性.

结论:

  • rCRUX是一个有效和用户友好的工具,用于为定制位置生成精选的,全面的DNA条形码参考数据库.
  • 该套件提高了元编码和DNA测序研究中的分类学分类的准确性和效率.
  • rCRUX解决了对生物多样性研究和监测领域专业参考图书馆日益增长的需求.