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

Size and Structure of Viral Genomes01:26

Size and Structure of Viral Genomes

301
Viral genomes exhibit remarkable diversity in size, structure, and composition, influencing their replication strategies and interactions with host cells. These genomes consist of either DNA or RNA and may be linear or circular. Additionally, they can be single-stranded or double-stranded, with each configuration affecting how the virus propagates within a host. RNA viruses, for instance, generally have smaller genomes than DNA viruses, a factor that contributes to their high mutation rates and...
301
Chromatin Packaging01:32

Chromatin Packaging

18.0K
Each human somatic cell contains 6 billion base pairs of DNA. Each base pair is 0.34 nm long, meaning each diploid cell contains a staggering 2 meters of DNA. This long DNA strand is packed inside a nucleus measuring only 10-20 microns in diameter with the help of specialized DNA-binding proteins called histones. Together they form a compact DNA-protein complex called chromatin. The chromatin is further compacted into higher-order structures. The highest level of compaction is achieved during...
18.0K
Chromatin Packaging02:21

Chromatin Packaging

18.1K
Each human somatic cell contains 6 billion base-pairs of DNA. Each base-pair is 0.34 nm long, which means that each diploid cell contains a staggering 2 meters of DNA. How is such a long DNA strand packed inside a nucleus measuring only 10 - 20 microns in diameter? 
The chromatin
In combination with specialized DNA binding protein called Histones, the DNA double helix forms a compact DNA: protein complex called chromatin. The chromatin itself is further compacted into higher-order...
18.1K
The Nucleosome01:19

The Nucleosome

3.1K
Human DNA is almost two meters long. However, it is compressed inside a tiny nucleus measuring only a few microns in diameter. To make this degree of compaction possible, DNA is organized into several sequential levels so that it can fit into such a tiny space. The most compact form of DNA is a chromosome that can be seen under a microscope in a dividing cell.
In a chromosome, DNA is wound twice around a protein complex called a histone octamer core, which consists of 8 histone proteins. This...
3.1K
Genome Size and the Evolution of New Genes03:21

Genome Size and the Evolution of New Genes

8.6K
While every living organism has a genome of some kind (be it RNA, or DNA), there is considerable variation in the sizes of these blueprints. One major factor that impacts genome size is whether the organism is prokaryotic or eukaryotic. In prokaryotes, the genome contains little to no non-coding sequence, such that genes are tightly clustered in groups or operons sequentially along the chromosome. Conversely, the genes in eukaryotes are punctuated by long stretches of non-coding sequence.
8.6K
Genome Size and the Evolution of New Genes03:21

Genome Size and the Evolution of New Genes

2.8K
2.8K

You might also read

Related Articles

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

Sort by
Same author

Data-driven AI system for learning how to run transcript assemblers.

Genome biology·2026
Same author

CodonMoE: DNA language models for codon-dependent mRNA prediction.

Bioinformatics (Oxford, England)·2026
Same author

CodonRL: Multi-Objective Codon Sequence Optimization Using Demonstration-Guided Reinforcement Learning.

bioRxiv : the preprint server for biology·2026
Same author

seq2ribo: Structure-aware integration of machine learning and simulation to predict ribosome location profiles from RNA sequences.

bioRxiv : the preprint server for biology·2026
Same author

Augmenting Electronic Health Records for Adverse Event Detection.

medRxiv : the preprint server for health sciences·2026
Same author

Crystalline Neutral Boraolympicenyl Radicals with Electronic Regulation through Boron-Doping Sites.

Journal of the American Chemical Society·2025
Same journal

conMItion: an R package adjusting confounding factors for associations in multi-omics.

Bioinformatics (Oxford, England)·2026
Same journal

SpaMFG: a Spatial Multi-omics Integration Method based on Feature Grouping.

Bioinformatics (Oxford, England)·2026
Same journal

CSCN: Inference of Cell-Specific Causal Networks Using Single-Cell RNA-Seq Data.

Bioinformatics (Oxford, England)·2026
Same journal

Sparse CCA-Based Mediation Analysis with High-Dimensional Exposures and Mediators.

Bioinformatics (Oxford, England)·2026
Same journal

Enhancing Cross-Context Generalization in Drug Perturbation Prediction with a Multimodal Conditional Diffusion Framework.

Bioinformatics (Oxford, England)·2026
Same journal

Primer Design through Submodular Function Estimation.

Bioinformatics (Oxford, England)·2026
See all related articles

Related Experiment Video

Updated: Oct 29, 2025

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

5.4K

Constructing small genome graphs via string compression.

Yutong Qiu1, Carl Kingsford1

  • 1Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA.

Bioinformatics (Oxford, England)
|July 12, 2021
PubMed
Summary
This summary is machine-generated.

Genome graph size impacts efficiency, necessitating space-saving methods. RLZ-Graph, using relative Lempel-Ziv, reduces genome graph storage by 40.7% compared to existing methods.

More Related Videos

Stable DNA Motifs, 1D and 2D Nanostructures Constructed from Small Circular DNA Molecules
09:32

Stable DNA Motifs, 1D and 2D Nanostructures Constructed from Small Circular DNA Molecules

Published on: April 12, 2019

6.8K
Rapid Assembly of Multi-Gene Constructs using Modular Golden Gate Cloning
08:31

Rapid Assembly of Multi-Gene Constructs using Modular Golden Gate Cloning

Published on: February 5, 2021

14.3K

Related Experiment Videos

Last Updated: Oct 29, 2025

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

5.4K
Stable DNA Motifs, 1D and 2D Nanostructures Constructed from Small Circular DNA Molecules
09:32

Stable DNA Motifs, 1D and 2D Nanostructures Constructed from Small Circular DNA Molecules

Published on: April 12, 2019

6.8K
Rapid Assembly of Multi-Gene Constructs using Modular Golden Gate Cloning
08:31

Rapid Assembly of Multi-Gene Constructs using Modular Golden Gate Cloning

Published on: February 5, 2021

14.3K

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Genome graph size is critical for efficient sequence alignment and other operations.
  • Current genome graph construction methods can be space-intensive, limiting their practical application.

Purpose of the Study:

  • To develop space-efficient genome graph construction methods.
  • To explore the application of compression models for genome graphs.
  • To introduce a novel genome graph construction algorithm and evaluate its performance.

Main Methods:

  • Developed linear-time algorithms to transform genome graphs into external pointer macro (EPM) compressed forms.
  • Proposed and formulated the source assignment problem as an integer linear programming (ILP) problem to optimize compression.
  • Implemented RLZ-Graph, a genome graph construction method based on the relative Lempel-Ziv algorithm.

Main Results:

  • Achieved an upper bound on genome graph size based on optimal EPM compression.
  • RLZ-Graph reduced disk space for human genome graphs by an average of 40.7% compared to compacted de Bruijn graphs (Bifrost).
  • RLZ-Graph demonstrated favorable scalability in runtime and graph size with increasing numbers of human genome sequences.

Conclusions:

  • RLZ-Graph offers a significant reduction in genome graph storage space.
  • The proposed methods provide a foundation for more efficient genome graph representations.
  • RLZ-Graph presents a scalable and effective alternative for constructing large-scale genome graphs.