Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

RNA-seq03:21

RNA-seq

12.3K
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...
12.3K
Ribosome Profiling02:24

Ribosome Profiling

4.2K
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.
The technique...
4.2K
Experimental RNAi02:15

Experimental RNAi

8.1K
RNA interference (RNAi) is a cellular mechanism that inhibits gene expression by suppressing its transcription or activating the RNA degradation process. The mechanism was discovered by Andrew Fire and Craig Mello in 1998 in plants. Today, it is observed in almost all eukaryotes, including protozoa, flies, nematodes, insects, parasites, and mammals. This precise cellular mechanism of gene silencing has been developed into a technique that provides an efficient way to identify and determine the...
8.1K
Viruses with RNA Genomes01:29

Viruses with RNA Genomes

1.1K
RNA viruses are categorized into positive-strand, negative-strand, or double-stranded groups based on their genomic structure and replication mechanisms. This classification dictates how they exploit host cellular machinery for protein synthesis and replication. Some RNA viruses also utilize reverse transcription as part of their life cycle, further diversifying their replication strategies.Positive-Strand RNA VirusesPositive-strand RNA viruses have genomes that function directly as messenger...
1.1K

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Discovery and analytical assessment of urinary miRNA biomarkers for cervical cancer using advanced small RNA sequencing.

Translational oncology·2026
Same author

An Integrative Framework Identifies Cooperative Targeting of Host Pathways by Tick Salivary miRNAs.

Computational and structural biotechnology journal·2026
Same author

SEOM-TTCC clinical guidelines for the treatment of head and neck cancer (2025).

Clinical & translational oncology : official publication of the Federation of Spanish Oncology Societies and of the National Cancer Institute of Mexico·2026
Same author

Mesenchymal Colorectal Cancers Secrete Vesicles With Unique Cargo That Can Be Used for Liquid Biopsy Based Diagnostics.

Journal of extracellular vesicles·2025
Same author

Genome Divergence Based on Entropic Segmentation of DNA.

Entropy (Basel, Switzerland)·2025
Same author

Knowing is not enough; we must apply: the case for rigorous microRNA annotation standards.

Nucleic acids research·2025
Same journal

Mapping the 3D Chromosome Organization of a Biosynthetic Gene Cluster by Capture Hi-C (CHi-C).

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

Mapping the 3D Chromosome Organization of Streptomyces by Hi-C.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

CUT&Tag Epigenomic Profiling of Biosynthetic Gene Clusters in Arabidopsis thaliana.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

Rhizobium rhizogenes-Mediated Hairy Root Transformation Protocol for Lotus japonicus and Other Legumes.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

Characterization of Bioactive Saponins from Sea Cucumbers.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

Methods for Functional Validation of Terpenoid Metabolic Clusters in Nicotiana benthamiana and Aspergillus oryzae.

Methods in molecular biology (Clifton, N.J.)·2026
See all related articles

Related Experiment Video

Updated: Mar 3, 2026

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
10:34

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells

Published on: December 9, 2022

5.3K

sRNAtoolboxVM: Small RNA Analysis in a Virtual Machine.

Cristina Gómez-Martín1, Ricardo Lebrón1,2, Antonio Rueda3

  • 1Dpto. de Genética, Facultad de Ciencias, Universidad de Granada, Campus de Fuentenueva s/n, 18071, Granada, Spain.

Methods in Molecular Biology (Clifton, N.J.)
|April 26, 2017
PubMed
Summary
This summary is machine-generated.

High-throughput sequencing (HTS) generates vast small RNA data. sRNAtoolboxVM offers a cost-effective Linux environment for analysis, overcoming computational bottlenecks for researchers.

Keywords:
BioinformaticsNext generation sequencingSmall RNAVirtual machine

More Related Videos

Rup (RNA-seq Usability Assessment Pipeline) - Quality Control for Bulk RNA-seq Experiments in Eukaryotes
05:07

Rup (RNA-seq Usability Assessment Pipeline) - Quality Control for Bulk RNA-seq Experiments in Eukaryotes

Published on: November 7, 2025

452
Measuring mRNA Levels Over Time During the Yeast S. cerevisiae Hypoxic Response
09:45

Measuring mRNA Levels Over Time During the Yeast S. cerevisiae Hypoxic Response

Published on: August 10, 2017

8.7K

Related Experiment Videos

Last Updated: Mar 3, 2026

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
10:34

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells

Published on: December 9, 2022

5.3K
Rup (RNA-seq Usability Assessment Pipeline) - Quality Control for Bulk RNA-seq Experiments in Eukaryotes
05:07

Rup (RNA-seq Usability Assessment Pipeline) - Quality Control for Bulk RNA-seq Experiments in Eukaryotes

Published on: November 7, 2025

452
Measuring mRNA Levels Over Time During the Yeast S. cerevisiae Hypoxic Response
09:45

Measuring mRNA Levels Over Time During the Yeast S. cerevisiae Hypoxic Response

Published on: August 10, 2017

8.7K

Area of Science:

  • Bioinformatics
  • Genomics
  • Molecular Biology

Background:

  • High-throughput sequencing (HTS) for small RNAs is accessible, but data analysis presents a significant bottleneck.
  • Linux environments, often required for analysis, incur substantial costs for hardware, system administration, and bioinformaticians, limiting access for smaller research groups.
  • Web servers offer an alternative but have limitations in flexibility and are unsuitable for sensitive medical data.

Purpose of the Study:

  • To present a protocol for utilizing virtual machines to overcome the challenges in small RNA data analysis.
  • To introduce sRNAtoolboxVM as a solution for accessible and flexible small RNA data analysis.

Main Methods:

  • Development and implementation of sRNAtoolboxVM, a virtual machine.
  • Preinstallation of essential bioinformatics tools, including sRNAbench, within the virtual machine.

Main Results:

  • sRNAtoolboxVM provides a preconfigured Linux environment for small RNA analysis.
  • It eliminates the need for dedicated servers and complex operating system management.
  • Enables researchers to perform a wide range of analyses using pre-installed software.

Conclusions:

  • Virtual machines, specifically sRNAtoolboxVM, offer a practical and cost-effective solution to the computational challenges in small RNA data analysis.
  • This approach democratizes access to advanced bioinformatics tools for researchers with limited resources.
  • Facilitates routine and comprehensive analysis of small RNA sequencing data.