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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.

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Last Updated: Jul 12, 2025

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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.