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

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 microarray-based...
Ribosome Profiling02:24

Ribosome Profiling

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 helps...

You might also read

Related Articles

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

Sort by
Same author

Cyclophilin A-mediated cis/trans isomerization modulates RIN4 to control intracellular rhizobial infection in legumes.

The New phytologist·2026
Same author

The roots of nodules: a shared genetic infrastructure of root lateral organs suggests a common origin.

Journal of experimental botany·2026
Same author

KeySDL: sparse dictionary learning for keystone microbe identification from steady-state observations using a dynamical-systems model.

BioData mining·2026
Same author

The Lotus japonicus alpha-expansin EXPA1 is recruited during intracellular and intercellular rhizobial colonization.

The Plant journal : for cell and molecular biology·2025
Same author

Genome-wide association study identifies candidate genes contributing to flowering time variation in <i>Lotus japonicus</i> in Japan.

Plant biotechnology (Tokyo, Japan)·2025
Same author

Two residues reprogram immunity receptors for nitrogen-fixing symbiosis.

Nature·2025
Same journal

Biomedical Concept Recognition with Error-aware Negative-enhanced Ranking Framework.

Bioinformatics (Oxford, England)·2026
Same journal

TEDLH: Domain HMMs for sensitive detection of remote homologues.

Bioinformatics (Oxford, England)·2026
Same journal

PLNFGL: Joint Estimation of Multi-Condition Gene Networks from Single-cell RNA-seq Data.

Bioinformatics (Oxford, England)·2026
Same journal

MCFST: Spatial domain identification method based on multi-view graph convolutional network and graph fusion network.

Bioinformatics (Oxford, England)·2026
Same journal

SpaBiT: Enhancing Spatial Transcriptomics Resolution via Bidirectional Attention Transformers.

Bioinformatics (Oxford, England)·2026
Same journal

EDEL: Enhancing Dense Retrievers for Curation of Biomedical Knowledge Bases.

Bioinformatics (Oxford, England)·2026
See all related articles

Related Experiment Video

Updated: May 19, 2026

A Complete Pipeline for Isolating and Sequencing MicroRNAs, and Analyzing Them Using Open Source Tools
09:29

A Complete Pipeline for Isolating and Sequencing MicroRNAs, and Analyzing Them Using Open Source Tools

Published on: August 21, 2019

shortran: a pipeline for small RNA-seq data analysis.

Vikas Gupta1, Katharina Markmann, Christian N S Pedersen

  • 1Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark. vgupta@cs.au.dk

Bioinformatics (Oxford, England)
|August 24, 2012
PubMed
Summary
This summary is machine-generated.

The shortran pipeline offers a flexible solution for analyzing plant and animal short RNA sequencing data. It aids in data mining by integrating visualization, annotation, and abundance profiling for complex hypothesis testing.

More Related Videos

AQRNA-seq for Quantifying Small RNAs
05:12

AQRNA-seq for Quantifying Small RNAs

Published on: February 2, 2024

Related Experiment Videos

Last Updated: May 19, 2026

A Complete Pipeline for Isolating and Sequencing MicroRNAs, and Analyzing Them Using Open Source Tools
09:29

A Complete Pipeline for Isolating and Sequencing MicroRNAs, and Analyzing Them Using Open Source Tools

Published on: August 21, 2019

AQRNA-seq for Quantifying Small RNAs
05:12

AQRNA-seq for Quantifying Small RNAs

Published on: February 2, 2024

Area of Science:

  • Bioinformatics
  • Genomics
  • Molecular Biology

Background:

  • High-throughput sequencing generates vast amounts of small RNA (sRNA) data, necessitating efficient data mining strategies.
  • Understanding sRNA function requires analyzing multidimensional data including length, abundance, sequence composition, and genomic location.

Purpose of the Study:

  • To develop a flexible pipeline for the analysis of plant and animal short RNA sequencing data.
  • To facilitate the generation and querying of disparate information for sRNA research.

Main Methods:

  • The shortran pipeline comprises nine modules designed for processing sRNA sequencing data.
  • It integrates visualization, annotation, and abundance profiling tools.
  • The pipeline supports flexible hypothesis testing and data querying.

Main Results:

  • The shortran pipeline enables comprehensive analysis of sRNA sequencing data.
  • It produces both graphical and MySQL format outputs for diverse applications.
  • Facilitates the exploration of sRNA function through multidimensional data analysis.

Conclusions:

  • shortran provides a valuable tool for researchers working with large sRNA datasets.
  • The pipeline enhances the ability to mine sRNA data for functional insights.
  • shortran supports flexible and integrated analysis of plant and animal sRNA sequencing data.