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

Genome Annotation and Assembly03:36

Genome Annotation and Assembly

21.2K
The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
21.2K
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

7.1K
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...
7.1K
Next-generation Sequencing03:00

Next-generation Sequencing

99.4K
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....
99.4K
Sanger Sequencing01:57

Sanger Sequencing

775.9K
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...
775.9K

You might also read

Related Articles

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

Sort by
Same author

Latent profiles of death coping competence among nursing interns and associations with death attitudes, death exposure, and death education; a cross-sectional survey.

International journal of nursing studies advances·2026
Same author

Epimedii Folium Supplementation Improves Semen Quality, Hormonal Profile, and Immune Function by Modulating Gut Microbiota and Seminal Metabolites in Aged Boars.

Animals : an open access journal from MDPI·2026
Same author

A novel role for magnetotactic bacterium: Magnetospirillum magneticum AMB-1 prolonged healthy lifespan of Caenorhabditis elegans via regulating ferroptosis.

Free radical biology & medicine·2026
Same author

Cumulus cells enhance oocyte genomic quality control by promoting DNA damage-induced meiotic arrest.

Journal of cell science·2026
Same author

Magnetotactic bacteria antagonized lead toxicity: Distinct detoxification mechanisms in magnetosome-containing/deficient bacteria.

Journal of environmental sciences (China)·2026
Same author

A Molecular-Protein Fusion Framework for Rapid Virtual Screening: Accelerating Lead Discovery for "Undruggable'' Oncogenic Targets.

Pharmaceuticals (Basel, Switzerland)·2026
Same journal

STED: flexible cross-modal topic modeling infers cell-type-specific regulatory landscapes from bulk epigenomics.

Briefings in bioinformatics·2026
Same journal

A knowledge-guided deep learning framework for quantitative nucleic acid testing.

Briefings in bioinformatics·2026
Same journal

Optimal transport for label transfer in single-cell multi-omics integration.

Briefings in bioinformatics·2026
Same journal

Continuous multi-omics pathway enrichment analysis resolves hidden functional heterogeneity.

Briefings in bioinformatics·2026
Same journal

Evaluating completeness, coherence, and consistency of genome-scale function annotations.

Briefings in bioinformatics·2026
Same journal

Transformers for single-cell RNA sequencing: a survey.

Briefings in bioinformatics·2026
See all related articles

Related Experiment Video

Updated: Feb 27, 2026

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies
12:08

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies

Published on: August 20, 2021

5.9K

Pangenome-guided sequence assembly via binary optimization.

Josh Cudby1,2, James Bonfield3, Chenxi Zhou4

  • 1Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Wilberforce Road, Cambridge CB3 0WA, United Kingdom.

Briefings in Bioinformatics
|February 26, 2026
PubMed
Summary
This summary is machine-generated.

We developed a new pangenome-guided genome assembly method to tackle complex, repetitive DNA regions. This approach optimizes graph traversal, offering a bias-free alternative to traditional de novo and reference-guided assemblers, with potential for quantum computing applications.

Keywords:
assemblyoptimizationpangenomicsquantum algorithms

More Related Videos

Novel Sequence Discovery by Subtractive Genomics
09:40

Novel Sequence Discovery by Subtractive Genomics

Published on: January 25, 2019

9.2K
Validating Whole Genome Nanopore Sequencing, using Usutu Virus as an Example
05:45

Validating Whole Genome Nanopore Sequencing, using Usutu Virus as an Example

Published on: March 11, 2020

9.4K

Related Experiment Videos

Last Updated: Feb 27, 2026

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies
12:08

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies

Published on: August 20, 2021

5.9K
Novel Sequence Discovery by Subtractive Genomics
09:40

Novel Sequence Discovery by Subtractive Genomics

Published on: January 25, 2019

9.2K
Validating Whole Genome Nanopore Sequencing, using Usutu Virus as an Example
05:45

Validating Whole Genome Nanopore Sequencing, using Usutu Virus as an Example

Published on: March 11, 2020

9.4K

Area of Science:

  • Genomics
  • Computational Biology
  • Bioinformatics

Background:

  • De novo genome assembly is difficult in repetitive regions.
  • Reference-guided assemblers can introduce bias.
  • Short-read data presents challenges for accurate genome reconstruction.

Purpose of the Study:

  • To propose a novel framework for pangenome-guided sequence assembly.
  • To address challenges in assembling complex and repetitive genomic regions.
  • To develop a bias-free assembly method adaptable for classical and quantum computing.

Main Methods:

  • Framing genome assembly as a graph traversal optimization problem.
  • Annotating pangenome graphs with estimated copy numbers.
  • Implementing optimization algorithms for pathfinding on graphs.
  • Developing tools for synthetic pangenome generation, read alignment, and assembly evaluation.

Main Results:

  • Significantly reduced contig count compared to de novo assemblers on simulated data.
  • Optimization-based methods are competitive with exhaustive search techniques.
  • Demonstrated resilience to noise in copy number estimation.
  • Showcased potential for quantum computing implementation with a small experiment on a real quantum device.

Conclusions:

  • The proposed pangenome-guided assembly framework effectively resolves complex genomic regions.
  • The optimization-based approach offers a scalable and bias-free alternative for genome assembly.
  • The method shows promise for future quantum computing applications in genomics.