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Related Concept Videos

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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Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing
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isolateR: an R package for generating microbial libraries from Sanger sequencing data.

Brendan Daisley1, Sarah J Vancuren1, Dylan J L Brettingham1

  • 1Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada.

Bioinformatics (Oxford, England)
|July 11, 2024
PubMed
Summary
This summary is machine-generated.

isolateR streamlines microbial identification by automating Sanger sequence processing and taxonomic classification. This enables efficient creation of strain libraries for cataloging microbial diversity and discovering novel species.

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Area of Science:

  • Microbiology
  • Bioinformatics

Background:

  • Sanger sequencing of marker genes is crucial for microbial identification (bacteria, archaea, fungi).
  • Manual processing and BLAST limitations hinder efficient strain library generation for microbial diversity studies.

Purpose of the Study:

  • To develop a standardized and scalable pipeline for automated processing of Sanger sequence data.
  • To facilitate the creation of comprehensive strain libraries for microbial cataloging and novel species discovery.

Main Methods:

  • Automated batch processing of Sanger sequence files.
  • Taxonomic classification using global alignment to type strain databases adhering to international nomenclature.
  • Creation of strain libraries with customizable dereplication and multi-run data integration.
  • Interactive HTML outputs for simplified data exploration.

Main Results:

  • isolateR successfully automates Sanger sequence analysis and taxonomic classification.
  • The tool enables efficient generation of strain libraries, crucial for microbial diversity cataloging.
  • Benchmarking on human gut datasets demonstrated isolateR's proficiency in uncovering nuanced microbial diversity at the strain level.

Conclusions:

  • isolateR addresses key challenges in microbial strain library generation.
  • The tool promotes a more targeted and granular approach to exploring microbial diversity within hosts.
  • isolateR facilitates the discovery of novel microbial species and enhances cataloging efforts.