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

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.
Assembly of Complex Microtubule Structures01:32

Assembly of Complex Microtubule Structures

Complex microtubule structures are present in resting cells and in dividing cells. In resting cells, they are responsible for maintaining the cellular architecture, tracks for intracellular transport, positioning of organelles, assembly of cilia and flagella. They mediate the bipolar spindle assembly for chromosomal segregation and positioning of the cell division plate in dividing cells. The formation of microtubule complex structures depends on the cell type, cell stage, and cell function.
Oligosaccharide Assembly01:24

Oligosaccharide Assembly

Protein glycosylation starts in the ER lumen and continues in the Golgi apparatus. Glycosyltransferases catalyze the addition of sugar molecules or glycosylation of proteins. Usually, these enzymes add sugars to the hydroxyl groups of selected serine or threonine residues to form O-linked glycans or the amino groups of asparagine residues to form N-linked glycans. Different positions on the same polypeptide chain can contain differently linked glycans.
Multiple sugar molecules that may or may...
Protein Complex Assembly02:41

Protein Complex Assembly

Proteins can form homomeric complexes with another unit of the same protein or heteromeric complexes with different types.  Most protein complexes self-assemble spontaneously via ordered pathways, while some proteins need assembly factors that guide their proper assembly. Despite the crowded intracellular environment, proteins usually interact with their correct partners and form functional complexes.
Many viruses self-assemble into a fully functional unit using the infected host cell to...
Protein Complex Assembly02:41

Protein Complex Assembly

Proteins can form homomeric complexes with another unit of the same protein or heteromeric complexes with different types.  Most protein complexes self-assemble spontaneously via ordered pathways, while some proteins need assembly factors that guide their proper assembly. Despite the crowded intracellular environment, proteins usually interact with their correct partners and form functional complexes.
Many viruses self-assemble into a fully functional unit using the infected host cell to...
Assembly of Cytoskeletal Filaments01:18

Assembly of Cytoskeletal Filaments

Cytoskeletal filaments are polymeric forms of smaller protein subunits. However, individual cytoskeletal filaments may easily disassemble or associate with other similar filaments to form rigid structures. Microfilaments, made of actin monomers, rely on actin-binding proteins to form bundles and create networks of individual actin filaments. Microtubules rely on microtubule-associated proteins (MAPs) to form sturdy cylindrical structures. However, the proteins involved in forming complex...

You might also read

Related Articles

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

Sort by
Same author

The role of gut microbiome in the pathophysiology of PTSD, depression, and anxiety disorders.

Gut microbes reports·2026
Same author

Being friendly to the skin microbiome: Experimental assessment.

Frontiers in microbiomes·2026
Same author

Babesia divergens and Babesia microti species-specific genes that may drive pathogenesis.

Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases·2026
Same author

Long-read sequencing reveals that the mitochondrial genome of an individual <i>Ixodiphagus hookeri</i> is a mixture of structural variants with an invariable core region and heterogeneous repeat regions.

Current research in parasitology & vector-borne diseases·2026
Same author

<i>Midichloria mitochondrii</i> stimulates the sylvatic cycle of <i>Borrelia burgdorferi</i> (<i>sensu lato</i>) in <i>Ixodes ricinus</i> and contributes to Lyme disease risk.

Current research in parasitology & vector-borne diseases·2025
Same author

Preliminary Insights Into the Relationship Between the Gut Microbiome and Host Genome in Posttraumatic Stress Disorder.

Genes, brain, and behavior·2025
Same journal

3DICE: Interpretable 3D Cross-Modal Learning for Drug-Target Interaction Prediction and Large-Scale Drug Discovery.

Bioinformatics (Oxford, England)·2026
Same journal

KASSPer: Kinase Active Site Structure Prediction using Protein and Ligand Language Models and Its Application to Virtual Screening.

Bioinformatics (Oxford, England)·2026
Same journal

IDR searcher: a search engine solution for public image resources.

Bioinformatics (Oxford, England)·2026
Same journal

KCFtools: Rapid alignment-free method for introgression screening and GWAS using k-mer profiles.

Bioinformatics (Oxford, England)·2026
Same journal

Meta2DB: Curated shotgun metagenomic feature sets and metadata for health state prediction.

Bioinformatics (Oxford, England)·2026
Same journal

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

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

Related Experiment Video

Updated: Jun 6, 2026

Reproducible Manufacturing of SPOT as a High-throughput Scaffold-based Culture Platform
06:22

Reproducible Manufacturing of SPOT as a High-throughput Scaffold-based Culture Platform

Published on: July 29, 2025

Scaffolding pre-assembled contigs using SSPACE.

Marten Boetzer1, Christiaan V Henkel, Hans J Jansen

  • 1BaseClear B.V., Einsteinweg 5, 2333 CC Leiden, Leiden,The Netherlands.

Bioinformatics (Oxford, England)
|December 15, 2010
PubMed
Summary
This summary is machine-generated.

This study introduces SSPACE, a new standalone tool for genome assembly. SSPACE effectively scaffolds contigs using paired-read data, significantly reducing the number of initial contigs in genomic datasets.

More Related Videos

Self-assembly of Complex Two-dimensional Shapes from Single-stranded DNA Tiles
10:23

Self-assembly of Complex Two-dimensional Shapes from Single-stranded DNA Tiles

Published on: May 8, 2015

Three-Dimensional Acoustic Assembly Device for Mass Manufacturing of Cell Spheroids
05:17

Three-Dimensional Acoustic Assembly Device for Mass Manufacturing of Cell Spheroids

Published on: October 13, 2023

Related Experiment Videos

Last Updated: Jun 6, 2026

Reproducible Manufacturing of SPOT as a High-throughput Scaffold-based Culture Platform
06:22

Reproducible Manufacturing of SPOT as a High-throughput Scaffold-based Culture Platform

Published on: July 29, 2025

Self-assembly of Complex Two-dimensional Shapes from Single-stranded DNA Tiles
10:23

Self-assembly of Complex Two-dimensional Shapes from Single-stranded DNA Tiles

Published on: May 8, 2015

Three-Dimensional Acoustic Assembly Device for Mass Manufacturing of Cell Spheroids
05:17

Three-Dimensional Acoustic Assembly Device for Mass Manufacturing of Cell Spheroids

Published on: October 13, 2023

Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • De novo assembly reconstructs genomes from next-generation sequencing (NGS) data, producing numerous contigs.
  • Scaffolding, which orders and connects contigs into larger structures, is vital for genome finishing but often integrated within assembly tools.
  • Independent control over scaffolding is limited with current integrated tools.

Purpose of the Study:

  • To present SSPACE, a novel, stand-alone scaffolding software.
  • To enable independent control over the scaffolding process using paired-read sequencing data.
  • To improve genome assembly by efficiently ordering and orienting contigs.

Main Methods:

  • Developed SSPACE as a stand-alone scaffolder utilizing paired-read sequencing data (paired-end and/or mate pair).
  • Incorporated features for short runtime and multiple library input.
  • Enabled contig extension using unmapped sequence reads.

Main Results:

  • SPSS enables efficient scaffolding of pre-assembled contigs.
  • The tool demonstrated a significant reduction in the initial contig count (at least 75%) on both prokaryotic and eukaryotic genomic datasets.
  • Achieved promising results in genome assembly quality.

Conclusions:

  • SPSS is an effective stand-alone tool for scaffolding contigs in genome assembly.
  • The software offers flexibility and efficiency for genomic research.
  • SPSS significantly improves genome reconstruction by reducing contig numbers.