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

Evolutionary Relationships through Genome Comparisons

Evolutionary Relationships through Genome Comparisons

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...

Comparing Copy Number Variations and SNPs

Comparing Copy Number Variations and SNPs

Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...

Sanger Sequencing

Sanger Sequencing

DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...

You might also read

Related Articles

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

Sort by

Same journal

Prioritising search for virtual screening via preliminary interpretable low-feature likelihood-based rankings of drug-target activity measures.

BMC bioinformatics·2026

Same journal

A novel attention mechanism for noise-adaptive and robust segmentation of microtubules in microscopy images.

BMC bioinformatics·2026

Same journal

Enhancing tumor T cell antigen prediction by integrating deep protein representations.

BMC bioinformatics·2026

Same journal

RiboZAP: a species-agnostic pipeline for rRNA depletion probe design in metatranscriptomics.

BMC bioinformatics·2026

Same journal

Model-based quantification of protein-protein interaction aberrations for exploring dysregulated signalling pathways through pathway maps and gene expression levels.

BMC bioinformatics·2026

Same journal

Research on multi-trait genome association study method based on Shannon information entropy.

BMC bioinformatics·2026

Search research articles

Related Experiment Video

Updated: Dec 31, 2025

An Integrated Approach for Microprotein Identification and Sequence Analysis

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

Alignment-free genomic sequence comparison using FCGR and signal processing.

Daniel Lichtblau¹

¹Wolfram Research, Champaign, 61820, Illinois, USA. danl@wolfram.com.

BMC Bioinformatics

|January 1, 2020

Summary

This study introduces a novel alignment-free genomic comparison method using Frequency Chaos Game Representation (FCGR) and dimension reduction techniques. The approach enables rapid sequence analysis, phylogenetic tree construction, and virus classification with high accuracy and scalability.

Keywords:

Alignment-free methods Chaos game representation Dimension reduction Genome comparison Genome identification Phylogenetic tree

More Related Videos

Author Spotlight: Cistrome Analysis in Mouse Muscle Stem Cells

Author Spotlight: Cistrome Analysis in Mouse Muscle Stem Cells

Published on: July 7, 2023

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture 4C-seq

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture 4C-seq

Published on: October 5, 2018

Related Experiment Videos

Last Updated: Dec 31, 2025

An Integrated Approach for Microprotein Identification and Sequence Analysis

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

Author Spotlight: Cistrome Analysis in Mouse Muscle Stem Cells

Author Spotlight: Cistrome Analysis in Mouse Muscle Stem Cells

Published on: July 7, 2023

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture 4C-seq

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture 4C-seq

Published on: October 5, 2018

Area of Science:

Genomics
Bioinformatics
Computational Biology

Background:

Alignment-free genomic comparison methods are crucial for analyzing large nucleotide sequence datasets.
These methods facilitate species identification and phylogenetic tree construction.

Purpose of the Study:

To present a novel, scalable, and accurate alignment-free genomic comparison method.
To demonstrate the method's effectiveness in sequence analysis, phylogenetic inference, and data classification.

Main Methods:

Utilizing Frequency Chaos Game Representation (FCGR) to convert nucleotide sequences into images.
Applying dimension reduction techniques, including Fourier transform and Singular Value Decomposition (SVD), to generate feature vectors.
Employing these vectors for sequence lookup, phylogenetic tree construction, and genomic data classification.

Main Results:

The FCGR combined with dimension reduction yields strong results for genomic comparison.
The method demonstrates high accuracy and scalability on benchmark datasets.
Applications include fast sequence identification, phylogenetic tree building, and virus genomic data classification.

Conclusions:

The FCGR and dimension reduction (Fourier transform, SVD) approach is a powerful tool for alignment-free genomic comparison.
This method's performance is competitive with, and often superior to, existing state-of-the-art techniques.
The approach exhibits excellent scalability for large genomic datasets.