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

Prokaryotic Gene Structure and Organization01:28

Prokaryotic Gene Structure and Organization

1.8K
Prokaryotic genomes exhibit a streamlined organization of coding and non-coding regions essential for gene expression and protein synthesis. While coding regions contain the genetic instructions for proteins or functional RNAs, non-coding regions regulate the precise transcription and translation of these genes.Coding Regions: Proteins and RNAsThe primary coding regions, known as structural genes, include sequences transcribed into messenger RNA (mRNA) and ultimately translated into...
1.8K
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

6.8K
Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
6.8K
Gene Evolution - Fast or Slow?02:05

Gene Evolution - Fast or Slow?

7.9K
The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...
7.9K
Organization of Genes02:07

Organization of Genes

73.0K
Overview
73.0K
Cis-regulatory Sequences02:02

Cis-regulatory Sequences

11.5K
Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
11.5K
Cis-regulatory Sequences02:02

Cis-regulatory Sequences

4.0K
4.0K

You might also read

Related Articles

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

Sort by
Same author

Harnessing Benzoyl-Urea Secondary-Sphere Hydrogen-Bonding to Enhance Oxygen Evolution Catalysis by Cobalt Corroles.

Small science·2026
Same author

Transcription factor 19 modulates fatty acid elongation and unfolded protein response to attenuate palmitic acid-induced hepatic dysfunction.

Nature communications·2026
Same author

Bioinformatics Approach to Cancer Prediction using Quantum Clustering Algorithm for Behavioral Similarity in Gene Expression.

Journal of visualized experiments : JoVE·2026
Same author

Cobalt(III) Corrolato Complexes with Tailored Secondary Spheres: Catalytic Implications for Water Oxidation.

Inorganic chemistry·2026
Same author

Protocol for 3D tumor spheroid generation, immunostaining, and imaging through comparative approaches.

STAR protocols·2025
Same author

ECM-Lamin Crosstalk in the Regulation of Genomic Stability.

Sub-cellular biochemistry·2025

Related Experiment Video

Updated: Jan 11, 2026

Single Cell Multiplex Reverse Transcription Polymerase Chain Reaction After Patch-clamp
10:44

Single Cell Multiplex Reverse Transcription Polymerase Chain Reaction After Patch-clamp

Published on: June 20, 2018

10.3K

Classification of coding and non-coding regions in eukaryotic gene sequences using an adaptive anti-notch filter

Atanu Mondal1, Subhajit Kar1, Madhabi Ganguly2

  • 1Dept. of Electronics, West Bengal State University, 126, Kolkata, India.

Computational Biology and Chemistry
|November 19, 2025
PubMed
Summary

This study introduces a novel genomic signal processing technique to accurately identify coding and non-coding regions in gene sequences. The method utilizes the period-3 characteristic of exons, achieving high accuracy in predicting protein-coding DNA segments.

Keywords:
Anti-notch filterBio-inspired algorithmCoding regionsGenomic signal processingPeriod-3 characteristic

More Related Videos

An Integrated Approach for Microprotein Identification and Sequence Analysis
09:37

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

3.9K
De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data
08:23

De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data

Published on: February 18, 2022

4.1K

Related Experiment Videos

Last Updated: Jan 11, 2026

Single Cell Multiplex Reverse Transcription Polymerase Chain Reaction After Patch-clamp
10:44

Single Cell Multiplex Reverse Transcription Polymerase Chain Reaction After Patch-clamp

Published on: June 20, 2018

10.3K
An Integrated Approach for Microprotein Identification and Sequence Analysis
09:37

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

3.9K
De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data
08:23

De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data

Published on: February 18, 2022

4.1K

Area of Science:

  • Genomics
  • Bioinformatics
  • Signal Processing

Background:

  • Accurate classification of coding regions in gene sequences is vital for understanding protein formation and biological functions.
  • Identifying coding regions is challenging due to their disparate distribution and low density in eukaryotic genomes.

Purpose of the Study:

  • To propose a data-independent and window length-independent genomic signal processing technique for predicting coding and non-coding regions.
  • To leverage the inherent period-3 characteristic of exons for improved classification accuracy.

Main Methods:

  • A finite impulse response-based anti-notch filter (ANF) was designed using a hybrid Salp-Swarm-Whale optimization algorithm to capture the period-3 frequency.
  • Gene sequences were converted to binary data using Voss representation and processed by the ANF.
  • Low-pass filtering and power spectral density estimation were employed to identify period-3 peaks indicative of coding regions.

Main Results:

  • The proposed method demonstrated sequence length independence, performing effectively on both short (∼100 bp) and long (∼1,000,000 bp) sequences.
  • Evaluation on a benchmark sequence (F56F11.4a) yielded an AUC of 0.98 and an accuracy of 0.954.
  • Testing on a diverse dataset (MOD191) of 191 sequences from various organisms resulted in an AUC of 0.91.

Conclusions:

  • The developed genomic signal processing technique effectively identifies coding and non-coding regions by exploiting the period-3 characteristic of exons.
  • The method's robustness across different sequence lengths and diverse organisms highlights its potential for broad genomic analysis.
  • This approach offers a promising tool for accurate gene sequence classification in bioinformatics and genomics research.