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相关概念视频

RACE - Rapid Amplification of cDNA Ends02:35

RACE - Rapid Amplification of cDNA Ends

6.4K
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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RNA-seq03:21

RNA-seq

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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...
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Giant spider neurons uncover a myelin-derived waste-internalizing canal system that fails in neurodegeneration.

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rCRUX: A Rapid and Versatile Tool for Generating Metabarcoding Reference libraries in R.

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相关实验视频

Updated: Jul 24, 2025

Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing
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Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing

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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.

bioRxiv : the preprint server for biology
|July 3, 2023
PubMed
概括
此摘要是机器生成的。

创建全面的DNA条形码参考数据库对于准确的分类学赋值至关重要. 新的rCRUX R包简化了为任何基因区域生成这些必要资源,改善了元编码和DNA测序工作.

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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:

  • 准确的分类学分配依赖于精心策划的,全面的DNA条形码参考数据库.
  • 目前的数据库生成是具有挑战性的,因为大量的DNA序列数据和不断变化的目标.
  • 监测和研究需要不同的基因区域和种类,超出专业策划能力.

研究的目的:

  • 开发一个易于实施的工具,用于为任何定制的位置生成全面的元编码参考库.
  • 在R中呈现rCRUX包,从Anacapa工具包中重新构想CRUX工具.
  • 为了在元编码和DNA测序中促进准确的分类学分类.

主要方法:

  • 使用in silico PCR (get_seeds_local/get_seeds_remote) 来找到带有用户定义的原料的种子.
  • 使用代BLAST搜索 (blast_seeds) 与NCBI数据库进行分层随机抽样.
  • 应用数据库删除复制和清理 (derep_and_clean_db) 来确保分类学准确性.

主要成果:

  • 对于测试的位置,rCRUX产生了比CRABS,METACURATOR,RESCRIPt和ECOPCR更全面的参考数据库.
  • 成功创建了16个参考数据库,用于以前未经修复的元编码位置.
  • 证明了rCRUX在制作精心策划,全面,初始化特定参考条形码序列中的实用性.

结论:

  • rCRUX是一个用户友好的工具,用于创建定制的,全面的DNA参考数据库.
  • 提高了metabarcoding研究中的分类学分类的准确性和有效性.
  • 解决了对分子生态学和生物多样性监测领域专业参考图书馆的日益增长的需求.