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

Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

7.2K
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...
7.2K
Karyotyping01:17

Karyotyping

70.1K
Overview
70.1K
Modern Molecular Taxonomy01:29

Modern Molecular Taxonomy

837
Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...
837
Next-generation Sequencing03:00

Next-generation Sequencing

101.5K
The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features....
101.5K
Synteny and Evolution02:31

Synteny and Evolution

4.0K
John H. Renwick first coined the term “synteny” in 1971, which refers to the genes present on the same chromosomes, even if they are not genetically linked. The species with common ancestry tend to show conserved syntenic regions. Therefore, the concept of synteny is nowadays used to describe the evolutionary relationship between species.
Around 80 million years ago, the human and mice lineages diverged from the common ancestor. During the course of evolution, the ancestral...
4.0K
Single Nucleotide Polymorphisms-SNPs01:05

Single Nucleotide Polymorphisms-SNPs

19.9K
A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...
19.9K

You might also read

Related Articles

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

Sort by
Same author

Closing the Complexity Gap of the Double Distance Problem.

IEEE transactions on computational biology and bioinformatics·2025
Same author

Reconstructing rearrangement phylogenies of natural genomes.

Algorithms for molecular biology : AMB·2025
Same author

Panacus: fast and exact pangenome growth and core size estimation.

Bioinformatics (Oxford, England)·2024
Same author

Applying rearrangement distances to enable plasmid epidemiology with pling.

Microbial genomics·2024
Same author

Panacus: fast and exact pangenome growth and core size estimation.

bioRxiv : the preprint server for biology·2024
Same author

Family-Free Genome Comparison.

Methods in molecular biology (Clifton, N.J.)·2024

Related Experiment Video

Updated: Apr 4, 2026

Flow-sorting and Exome Sequencing of the Reed-Sternberg Cells of Classical Hodgkin Lymphoma
08:53

Flow-sorting and Exome Sequencing of the Reed-Sternberg Cells of Classical Hodgkin Lymphoma

Published on: June 10, 2017

10.6K

Sorting Linear Genomes with Rearrangements and Indels.

Marília D V Braga, Jens Stoye

    IEEE/ACM Transactions on Computational Biology and Bioinformatics
    |September 11, 2015
    PubMed
    Summary

    Genome rearrangement analysis is simplified by a new proof showing the Double Cut and Join (DCJ)-indel distance is the same for restricted and unrestricted models. This leads to a more efficient algorithm for genome sorting.

    Area of Science:

    • Comparative genomics
    • Bioinformatics
    • Computational biology

    Background:

    • Genome rearrangements like inversions and translocations alter genome organization but not content.
    • The Double Cut and Join (DCJ) operation models these rearrangements, with a restricted version (ER composition) for linear genomes.
    • Comparing genomes with unequal content requires considering insertions and deletions (indels) alongside rearrangements.

    Purpose of the Study:

    • To solve an open problem regarding the restricted DCJ-indel distance for linear genomes.
    • To present a simple proof that the unrestricted and restricted DCJ-indel distances are identical.
    • To develop a more efficient algorithm for computing the restricted DCJ-indel sorting scenario.

    Main Methods:

    • Mathematical modeling of genome rearrangements and indel operations.

    More Related Videos

    Detecting Somatic Genetic Alterations in Tumor Specimens by Exon Capture and Massively Parallel Sequencing
    11:02

    Detecting Somatic Genetic Alterations in Tumor Specimens by Exon Capture and Massively Parallel Sequencing

    Published on: October 18, 2013

    20.0K
    Amplification, Next-generation Sequencing, and Genomic DNA Mapping of Retroviral Integration Sites
    09:31

    Amplification, Next-generation Sequencing, and Genomic DNA Mapping of Retroviral Integration Sites

    Published on: March 22, 2016

    18.5K

    Related Experiment Videos

    Last Updated: Apr 4, 2026

    Flow-sorting and Exome Sequencing of the Reed-Sternberg Cells of Classical Hodgkin Lymphoma
    08:53

    Flow-sorting and Exome Sequencing of the Reed-Sternberg Cells of Classical Hodgkin Lymphoma

    Published on: June 10, 2017

    10.6K
    Detecting Somatic Genetic Alterations in Tumor Specimens by Exon Capture and Massively Parallel Sequencing
    11:02

    Detecting Somatic Genetic Alterations in Tumor Specimens by Exon Capture and Massively Parallel Sequencing

    Published on: October 18, 2013

    20.0K
    Amplification, Next-generation Sequencing, and Genomic DNA Mapping of Retroviral Integration Sites
    09:31

    Amplification, Next-generation Sequencing, and Genomic DNA Mapping of Retroviral Integration Sites

    Published on: March 22, 2016

    18.5K
  • Development and analysis of algorithms for calculating genomic distances.
  • Comparison of DCJ-indel distance with restricted DCJ-substitution distance.

    • Main Results:

    • A simple proof demonstrates that the DCJ-indel distance is the same for both unrestricted and restricted (ER composition) models.
    • A new, simpler algorithm computes the optimal restricted DCJ-indel sorting scenario in O(n log n) time.
    • The DCJ-indel distance is shown to be a 2-approximation for the restricted DCJ-substitution distance.

    Conclusions:

    • The study unifies the understanding of DCJ-indel distance in both restricted and unrestricted models for linear genomes.
    • The findings provide a more computationally efficient method for genome sorting and analysis.
    • The relationship established with DCJ-substitution distance offers insights into evolutionary processes involving larger DNA segment changes.