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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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Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
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Related Experiment Video

Updated: Nov 24, 2025

RIBO-seq in Bacteria: a Sample Collection and Library Preparation Protocol for NGS Sequencing
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RIBO-seq in Bacteria: a Sample Collection and Library Preparation Protocol for NGS Sequencing

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ProkSeq for complete analysis of RNA-Seq data from prokaryotes.

A K M Firoj Mahmud1, Nicolas Delhomme2, Soumyadeep Nandi3

  • 1Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Department of Molecular Biology, Umeå University, SE-901 87 Umeå, Sweden.

Bioinformatics (Oxford, England)
|December 28, 2020
PubMed
Summary
This summary is machine-generated.

ProkSeq is a new, automated RNA-Seq analysis pipeline for prokaryotes. It addresses the lack of tools for analyzing gene expression in bacteria under extreme conditions, offering comprehensive data analysis and visualization.

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Characterization of In Vitro Differentiation of Human Primary Keratinocytes by RNA-Seq Analysis
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Area of Science:

  • Microbiology
  • Bioinformatics
  • Genomics

Background:

  • RNA-Seq technology is widely used for bacterial gene expression studies.
  • Existing tools often lack capabilities for extreme conditions and comprehensive analysis.

Purpose of the Study:

  • To introduce ProkSeq, an automated RNA-Seq analysis pipeline.
  • To provide a user-friendly solution for prokaryotic gene expression analysis.

Main Methods:

  • ProkSeq is implemented in Python and available as a Docker container or via Anaconda.
  • The pipeline offers options for differential expression analysis, data normalization, and visualization.

Main Results:

  • ProkSeq provides a user-friendly, automated solution for prokaryotic RNA-Seq data.
  • The pipeline facilitates comprehensive analysis of gene expression differences.

Conclusions:

  • ProkSeq enhances the study of pathogenic bacteria by enabling detailed gene expression analysis.
  • The tool supports researchers working with prokaryotes under diverse conditions.