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

Phosphodiester Linkages01:01

Phosphodiester Linkages

110.7K
Overview
Phosphodiester bond forms when a phosphoric acid molecule (H3PO4) links with two hydroxyl groups (–OH) of two other molecules, forming two ester bonds. Two water molecules are released in this process. The phosphodiester bond is commonly found in nucleic acids (DNA and RNA) and plays a critical role in their structure and function.
Phosphodiester Bonds Link Nucleotides Together
DNA and RNA are polynucleotides or long chains of nucleotides that are linked together. A nucleotide is...
110.7K
Ligand Binding and Linkage00:49

Ligand Binding and Linkage

5.5K
Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked.  In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence...
5.5K
Ligand Binding and Linkage00:49

Ligand Binding and Linkage

4.0K
4.0K
Uncertainty in Measurement: Reading Instruments02:46

Uncertainty in Measurement: Reading Instruments

51.0K
Counting is the type of measurement that is free from uncertainty, provided the number of objects being counted does not change during the process. Such measurements result in exact numbers. By counting the eggs in a carton, for instance, one can determine exactly how many eggs are there in the carton. Similarly, the numbers of defined quantities are also exact. For example, 1 foot is exactly 12 inches, 1 inch is exactly 2.54 centimeters, and 1 gram is exactly 0.001 kilograms. Quantities...
51.0K
Protein Complex Assembly02:41

Protein Complex Assembly

16.7K
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...
16.7K
Spindle Assembly02:50

Spindle Assembly

4.2K
Spindle assembly occurs through three, often coexisting, pathways – the centrosome-mediated pathway, the chromatin-mediated pathway, and the microtubule-mediated pathway – collectively contributing to form a robust spindle apparatus.
In most cells, centrosomes are the primary microtubule nucleation centers. In the centrosome-mediated pathway, the G2-prophase transition triggers centrosome maturation and increased microtubule nucleation. Progressive nucleation results in a...
4.2K

You might also read

Related Articles

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

Sort by
Same author

Optimising Exome Captures in Species With Large Genomes Using Species-Specific Repetitive DNA Blocker.

Molecular ecology resources·2024
Same author

Heterogeneous genomic architecture of skeletal armour traits in sticklebacks.

Journal of evolutionary biology·2024
Same author

Improved assembly of the Pungitius pungitius reference genome.

G3 (Bethesda, Md.)·2024
Same author

The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars.

Nature genetics·2024
Same author

Space-efficient computation of k-mer dictionaries for large values of k.

Algorithms for molecular biology : AMB·2024
Same author

A revamped rat reference genome improves the discovery of genetic diversity in laboratory rats.

Cell genomics·2024
Same journal

Haplotype-aware long-read error correction.

Algorithms for molecular biology : AMB·2026
Same journal

Extension of partial atom-to-atom maps: uniqueness and algorithms.

Algorithms for molecular biology : AMB·2026
Same journal

Lossless pangenome indexing using tag arrays.

Algorithms for molecular biology : AMB·2026
Same journal

Dolphyin: a combinatorial algorithm for identifying 1-Dollo phylogenies in cancer.

Algorithms for molecular biology : AMB·2026
Same journal

Probing transcription factor subsets in gene regulatory networks.

Algorithms for molecular biology : AMB·2026
Same journal

Comparing the ability of embedding methods on metabolic hypergraphs for capturing taxonomy-based features.

Algorithms for molecular biology : AMB·2026
See all related articles

Related Experiment Video

Updated: Jan 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

5.8K

Kermit: linkage map guided long read assembly.

Riku Walve1, Pasi Rastas2, Leena Salmela1

  • 11Department of Computer Science, Helsinki Institute for Information Technology HIIT, University of Helsinki, Helsinki, Finland.

Algorithms for Molecular Biology : AMB
|April 2, 2019
PubMed
Summary
This summary is machine-generated.

This study introduces the first automated method to integrate linkage maps into genome assembly, improving contiguity and correctness. The approach simplifies the assembly graph, reducing errors in de novo assembly of long reads.

Keywords:
Coloured overlap graphGenome assemblyLinkage maps

More Related Videos

Decomposing the Variance in Reading Comprehension to Reveal the Unique and Common Effects of Language and Decoding
06:33

Decomposing the Variance in Reading Comprehension to Reveal the Unique and Common Effects of Language and Decoding

Published on: October 11, 2018

7.2K
A Practical Approach to Genetic Inducible Fate Mapping: A Visual Guide to Mark and Track Cells In Vivo
13:36

A Practical Approach to Genetic Inducible Fate Mapping: A Visual Guide to Mark and Track Cells In Vivo

Published on: December 30, 2009

17.3K

Related Experiment Videos

Last Updated: Jan 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

5.8K
Decomposing the Variance in Reading Comprehension to Reveal the Unique and Common Effects of Language and Decoding
06:33

Decomposing the Variance in Reading Comprehension to Reveal the Unique and Common Effects of Language and Decoding

Published on: October 11, 2018

7.2K
A Practical Approach to Genetic Inducible Fate Mapping: A Visual Guide to Mark and Track Cells In Vivo
13:36

A Practical Approach to Genetic Inducible Fate Mapping: A Visual Guide to Mark and Track Cells In Vivo

Published on: December 30, 2009

17.3K

Area of Science:

  • Genomics
  • Bioinformatics

Background:

  • Long-read sequencing is becoming more affordable, enabling large-scale projects.
  • De novo assembly of long reads is challenging due to high error rates and limited tools, often yielding fragmented assemblies.
  • Dense linkage maps offer long-range genomic information but their integration into automated assembly is lacking.

Purpose of the Study:

  • To develop the first automated method for guided genome assembly using linkage maps.
  • To improve the contiguity and correctness of genome assemblies derived from long reads.

Main Methods:

  • Formulated the genome assembly problem incorporating linkage map data.
  • Introduced a novel guided assembly method featuring an additional graph-cleaning step.
  • Evaluated the method's impact on assembly graph complexity and output quality.

Main Results:

  • The proposed method simplifies the genome assembly graph.
  • Achieved more contiguous assemblies compared to traditional de novo assembly.
  • Significantly reduced the number of misassemblies in the final genome assembly.

Conclusions:

  • Presented the first automated method for direct integration of linkage maps into genome assembly.
  • The method enhances genome assembly contiguity and correctness with minimal runtime increase.
  • This approach offers a powerful tool for improving long-read genome assembly.