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Related Concept Videos

Operons02:09

Operons

49.8K
Prokaryotes can control gene expression through operons—DNA sequences consisting of regulatory elements and clustered, functionally related protein-coding genes. Operons use a single promoter sequence to initiate transcription of a gene cluster (i.e., a group of structural genes) into a single mRNA molecule. The terminator sequence ends transcription. An operator sequence, located between the promoter and structural genes, prohibits the operon’s transcriptional activity if bound by...
49.8K
Operon Model01:23

Operon Model

118
The operon model represents a fundamental mechanism of gene regulation in prokaryotes, enabling coordinated expression of genes involved in related metabolic or functional pathways. Operons consist of structural genes, a promoter, and an operator, with transcription regulated by repressors, activators, and small effector molecules.Structure and Function of OperonsAn operon is a cluster of structural genes transcribed together under the control of a single promoter. The promoter region...
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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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Repressible Operon: trp Operon01:21

Repressible Operon: trp Operon

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The trp operon in Escherichia coli exemplifies a repressible operon. It regulates the synthesis of tryptophan through repressor-mediated transcriptional control and attenuation. This dual regulatory mechanism ensures tryptophan biosynthesis occurs only when needed, conserving cellular resources.Structure of the trp OperonThe trp operon consists of five structural genes (trpE, trpD, trpC, trpB, and trpA) that encode enzymes for tryptophan biosynthesis. These genes are transcribed as a single...
144
Ribosome Profiling02:24

Ribosome Profiling

3.6K
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...
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Inducible Operons: lac Operon01:25

Inducible Operons: lac Operon

157
The lac operon in Escherichia coli is a model for understanding inducible gene regulation and metabolic flexibility. It integrates local control by lactose and global regulation through catabolite repression, enabling E. coli to preferentially metabolize glucose when available and switch to lactose utilization when glucose is scarce.Structure and Function of the lac OperonThe lac operon contains three structural genes: lacZ (β-galactosidase), lacY (lactose permease), and lacA...
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Related Experiment Video

Updated: Sep 13, 2025

A Virtual Machine Platform for Non-Computer Professionals for Using Deep Learning to Classify Biological Sequences of Metagenomic Data
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OpDetect: A convolutional and recurrent neural network classifier for precise and sensitive operon detection from

Rezvan Karaji1, Lourdes Peña-Castillo1,2

  • 1Department of Computer Science, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador, Canada.

Plos One
|August 1, 2025
PubMed
Summary
This summary is machine-generated.

OpDetect is a new computational method for identifying bacterial operons using RNA-sequencing data. This deep learning approach offers improved accuracy and species-agnostic operon detection, advancing our understanding of gene regulation.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Operons are key genetic structures in prokaryotes, regulating gene function and expression.
  • Current operon detection methods often lack generalizability across species.
  • Accurate operon identification is crucial for understanding prokaryotic and some eukaryotic gene regulation.

Purpose of the Study:

  • To develop a general and accurate computational method for operon detection.
  • To leverage RNA-sequencing data for improved operon identification.
  • To create a species-agnostic tool applicable to diverse organisms.

Main Methods:

  • Developed OpDetect, a novel computational approach utilizing RNA-sequencing reads.
  • Employed a deep neural network architecture combining convolutional and recurrent layers.
  • Applied the method to analyze genomic data for operon identification.

Main Results:

  • OpDetect demonstrated superior performance in recall, F1-score, and AUROC compared to existing methods.
  • The method achieved high accuracy in operon detection across various bacterial species.
  • OpDetect successfully identified operons in the eukaryotic organism Caenorhabditis elegans.

Conclusions:

  • OpDetect provides a robust and versatile tool for operon detection.
  • The species-agnostic nature of OpDetect enhances its applicability in comparative genomics.
  • This method advances the study of gene organization and regulation in prokaryotes and beyond.