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

Gene Duplication and Divergence

Gene Duplication and Divergence

The seminal work of Ohno in 1970 popularized the idea of gene duplication and divergence. DNA sequence comparison studies reveal that a large portion of the genes in bacteria, archaebacteria, and eukaryotes was generated by gene duplication and divergence, indicating its critical role in evolution.
The duplicated copies of the gene are called Paralogs. Paralogs with similar sequences and functions form a gene family. Across several species, a large number of gene families are characterized.

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...

Gene Conversion

Gene Conversion

Other than maintaining genome stability via DNA repair, homologous recombination plays an important role in diversifying the genome. In fact, the recombination of sequences forms the molecular basis of genomic evolution. Random and non-random permutations of genomic sequences create a library of new amalgamated sequences. These newly formed genomes can determine the fitness and survival of cells. In bacteria, homologous and non-homologous types of recombination lead to the evolution of new...

Overview of Transposition and Recombination

Overview of Transposition and Recombination

Transposons make up a significant part of genomes of various organisms. Therefore, it is believed that transposition played a major evolutionary role in speciation by changing genome sizes and modifying gene expression patterns. For example, in bacteria, transposition can lead to conferring antibiotic resistance. Movement of transposable elements within the genetic pool of pathogenic bacteria can aid in transfer of antibiotic-resistant genetic elements. In eukaryotes, transposons can carry out...

Conservative Site-specific Recombination and Phase Variation

Conservative Site-specific Recombination and Phase Variation

Because the DNA segments are cut and reorganized in a direction-specific manner, site-specific recombination has emerged as an efficient genetic engineering technique. Flippase and Cyclization recombinases or Flp and Cre, respectively, are two members of the tyrosine recombinase family derived from bacteriophages, that are used to mediate site-specific DNA insertions, deletions, and targeted expression of proteins in mammalian cell lines.
The recognition sites for Cre recombinase called LoxP...

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%...

You might also read

Related Articles

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

Sort by

Same author

<i>SpecPeptidOMS</i> Directly and Rapidly Aligns Mass Spectra on Whole Proteomes and Identifies Peptides That Are Not Necessarily Tryptic: Implications for Peptidomics.

Journal of proteome research·2025

Same author

Partition Based Algorithms for Rearrangement Distances With Flexible Intergenic Regions.

IEEE transactions on computational biology and bioinformatics·2024

Same author

Fast alignment of mass spectra in large proteomics datasets, capturing dissimilarities arising from multiple complex modifications of peptides.

BMC bioinformatics·2023

Same author

Reversal and Transposition Distance on Unbalanced Genomes Using Intergenic Information.

Journal of computational biology : a journal of computational molecular cell biology·2023

Same author

MAGNETO: An Automated Workflow for Genome-Resolved Metagenomics.

mSystems·2022

Same author

Sorting Permutations by Intergenic Operations.

IEEE/ACM transactions on computational biology and bioinformatics·2021

Search research articles

Related Experiment Video

Updated: Jul 14, 2026

VDJ-Seq: Deep Sequencing Analysis of Rearranged Immunoglobulin Heavy Chain Gene to Reveal Clonal Evolution Patterns of B Cell Lymphoma

VDJ-Seq: Deep Sequencing Analysis of Rearranged Immunoglobulin Heavy Chain Gene to Reveal Clonal Evolution Patterns of B Cell Lymphoma

Published on: December 28, 2015

A pseudo-boolean framework for computing rearrangement distances between genomes with duplicates.

Sébastien Angibaud¹, Guillaume Fertin, Irena Rusu

¹Laboratoire d'Informatique de Nantes-Atlantique, FRE CNRS 2729, Université de Nantes, 2 rue de la Houssinière, 44322 Nantes Cedex 3, France. Sebastien.Angibaud@univ-nantes.fr

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology

|June 19, 2007

Summary

This study introduces a new pseudo-boolean method to calculate exact genomic distances, addressing the challenge of duplications in comparative genomics. The approach offers accurate solutions where previous heuristics fell short.

More Related Videos

G2-seq: A High Throughput Sequencing-based Technique for Identifying Late Replicating Regions of the Genome

G2-seq: A High Throughput Sequencing-based Technique for Identifying Late Replicating Regions of the Genome

Published on: March 22, 2018

Related Experiment Videos

Last Updated: Jul 14, 2026

VDJ-Seq: Deep Sequencing Analysis of Rearranged Immunoglobulin Heavy Chain Gene to Reveal Clonal Evolution Patterns of B Cell Lymphoma

VDJ-Seq: Deep Sequencing Analysis of Rearranged Immunoglobulin Heavy Chain Gene to Reveal Clonal Evolution Patterns of B Cell Lymphoma

Published on: December 28, 2015

G2-seq: A High Throughput Sequencing-based Technique for Identifying Late Replicating Regions of the Genome

G2-seq: A High Throughput Sequencing-based Technique for Identifying Late Replicating Regions of the Genome

Published on: March 22, 2018

Area of Science:

Computational Biology
Genomics
Bioinformatics

Background:

Comparative genomics relies on computing genomic distances between whole genomes.
Existing distance metrics include breakpoints, common/conserved intervals, and Maximum Adjacency Disruption number.
Many genomic distance problems become NP-hard in the presence of duplications, leading to heuristic solutions with unknown accuracy.

Purpose of the Study:

To develop an algorithmic approach for computing exact genomic distances in the presence of duplications.
To evaluate the accuracy of genomic distance heuristics.
To emphasize common intervals under the maximum matching model.

Main Methods:

A novel generic pseudo-boolean approach for exact genomic distance computation.
Focus on common intervals within the maximum matching model.
Testing of three heuristics on a gamma-Proteobacteria dataset.

Main Results:

The proposed pseudo-boolean method provides an exact solution for genomic distances with duplications.
Demonstrated the effectiveness of heuristics on a real-world dataset.
Highlighted the importance of common intervals in genomic distance calculations.

Conclusions:

The developed pseudo-boolean approach offers a significant advancement for accurate genomic distance computation.
The study provides a benchmark for evaluating heuristic methods in comparative genomics.
Accurate genomic distance calculation is crucial for understanding genome evolution and structure.