Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Reporter Genes

Reporter Genes

Reporter genes are a type of protein-coding gene that are often tagged to a gene of interest. Once inside a target cell, reporter genes usually produce visually identifiable characteristics like fluorescence and luminescence when expressed along with the gene of interest. Thus, reporter genes “report” the presence or absence of genes of interest in an organism, determine the gene expression pattern, or track the physical location of a DNA segment or protein in the cell.

Ribosome Profiling

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...

You might also read

Related Articles

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

Sort by

Same author

PyamilySeq: exposing the fragility of conventional gene (re)clustering and prokaryotic pangenomic inference methods.

NAR genomics and bioinformatics·2026

Same author

Coping with Ineffective Overlap in Multilocus Phylogenetics.

Systematic biology·2025

Same author

Lineage-specific microbial protein prediction enables large-scale exploration of protein ecology within the human gut.

Nature communications·2025

Same author

Heuristics for the run-length encoded Burrows-Wheeler transform alphabet ordering problem.

Journal of heuristics·2025

Same author

Accessory genes define species-specific routes to antibiotic resistance.

Life science alliance·2024

Same author

Improving Orthologous Signal and Model Fit in Datasets Addressing the Root of the Animal Phylogeny.

Molecular biology and evolution·2023

Same journal

Correction to 'New origin firing is inhibited by APC/CCdh1 activation in S-phase after severe replication stress'.

Nucleic acids research·2026

Same journal

VeloRM: disentangling pre- and post-splicing RNA modification dynamics at single-cell resolution.

Nucleic acids research·2026

Same journal

Accessibility of telomeric overhangs to stabilizing small-molecule ligands.

Nucleic acids research·2026

Same journal

Multivalent interactions mediate SNAIL transcription factor stimulation of the nucleosome deacetylase activity of the CoREST complex.

Nucleic acids research·2026

Same journal

Genome-wide mapping of DNA G-quadruplexes in Trypanosoma brucei chromatin reveals enrichment in coding regions and transcription start sites.

Nucleic acids research·2026

Same journal

Correction to 'The Gene Ontology knowledgebase in 2026'.

Nucleic acids research·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Jul 12, 2025

Mapping Bacterial Functional Networks and Pathways in Escherichia Coli using Synthetic Genetic Arrays

Mapping Bacterial Functional Networks and Pathways in Escherichia Coli using Synthetic Genetic Arrays

Published on: November 12, 2012

StORF-Reporter: finding genes between genes.

Nicholas J Dimonaco^1,2,3,4,5, Amanda Clare², Kim Kenobi⁶

¹Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth SY23 3PD, Wales, UK.

Nucleic Acids Research

|October 28, 2023

Summary

This summary is machine-generated.

StORF-Reporter identifies missing prokaryotic genes in unannotated genomic regions. This tool finds Stop-ORFs (StORFs), recovering genes often missed by standard annotation methods, improving genome annotation accuracy.

More Related Videos

Using Coculture to Detect Chemically Mediated Interspecies Interactions

Using Coculture to Detect Chemically Mediated Interspecies Interactions

Published on: October 31, 2013

A Fluorescence-based Method to Study Bacterial Gene Regulation in Infected Tissues

A Fluorescence-based Method to Study Bacterial Gene Regulation in Infected Tissues

Published on: February 19, 2019

Related Experiment Videos

Last Updated: Jul 12, 2025

Mapping Bacterial Functional Networks and Pathways in Escherichia Coli using Synthetic Genetic Arrays

Mapping Bacterial Functional Networks and Pathways in Escherichia Coli using Synthetic Genetic Arrays

Published on: November 12, 2012

Using Coculture to Detect Chemically Mediated Interspecies Interactions

Using Coculture to Detect Chemically Mediated Interspecies Interactions

Published on: October 31, 2013

A Fluorescence-based Method to Study Bacterial Gene Regulation in Infected Tissues

A Fluorescence-based Method to Study Bacterial Gene Regulation in Infected Tissues

Published on: February 19, 2019

Area of Science:

Genomics
Bioinformatics
Computational Biology

Background:

Prokaryotic genomes contain large unannotated regions due to annotation tool limitations.
Alternative start codons frequently cause misreporting or omission of genes in current annotations.

Purpose of the Study:

To present StORF-Reporter, a novel tool for identifying missing protein-coding genes (CDS) in unannotated prokaryotic genomic regions.
To improve the completeness and accuracy of prokaryotic genome annotations.

Main Methods:

Extraction of unannotated genomic regions from annotated genomes.
Identification of Stop-ORFs (StORFs) within these unannotated regions.
StORFs are open reading frames delimited by stop codons, designed to capture frequently missed genes.

Main Results:

StORF-Reporter successfully recovered genes absent from canonical genome annotations.
Application to model organisms, the Escherichia coli pangenome, and a large dataset (5109 genomes) revealed extended gene collections.
Novel gene families were identified, and existing families were extended across additional genera.

Conclusions:

The StORF-Reporter methodology effectively identifies and recovers potentially functional genes missed by standard annotation pipelines.
High sequence conservation across genera suggests many identified StORFs represent genuine functional genes.
These findings advocate for the inclusion of identified StORFs in future canonical genome annotations.