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.
Next-generation Sequencing03:00

Next-generation Sequencing

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.
RACE - Rapid Amplification of cDNA Ends02:35

RACE - Rapid Amplification of cDNA Ends

Rapid Amplification of cDNA Ends, or RACE, is one of the most effective methods to obtain a full-length cDNA from an mRNA sequence between a known internal region to the unknown sequence at the 5’ or 3’ end. The unknown region is cloned in the cDNA by a gene-specific primer that binds the known end, and a hybrid primer that attaches a predefined anchor sequence to the unknown end of the cDNA. The sequence in between is amplified by PCR with an anchor primer and a gene-specific primer.
Since the...
Sanger Sequencing01:57

Sanger Sequencing

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...
The Replisome03:01

The Replisome

DNA replication is carried out by a large complex of proteins that act in a coordinated matter to achieve high-fidelity DNA replication. Together this complex is known as the DNA replication machinery or the replisome.
The synthesis of the leading and lagging strands is a highly coordinated process. To explain this, the “Trombone model” was proposed by Bruce Alberts in 1980. The DNA loop formation starts when a primer is synthesized on the parent lagging strand. The loop grows with the...
Mismatch Repair01:36

Mismatch Repair

Overview

You might also read

Related Articles

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

Sort by
Same author

A k-mer-based estimator of the substitution rate between repetitive sequences.

Algorithms for molecular biology : AMB·2026
Same author

Dual-interface stabilization of low-iridium anodes for durable proton exchange membrane water electrolysis.

Nature communications·2026
Same author

High-dimensional immune profiling of peripheral blood identifies immune correlates of anti-PD-1/PD-L1 resistance in oncogenic driver mutation-positive NSCLC.

Frontiers in immunology·2026
Same author

Cross-species transcriptomic analysis of rodent model fidelity to human mesial temporal lobe epilepsy.

Nature communications·2026
Same author

Prognostic Impact of TP53 and RB1 Alterations in Metastatic Castration-Resistant Prostate Cancer Treated with Docetaxel.

Cancer investigation·2026
Same author

Microfluidic profiling of suspension cell-metal adhesion at single-cell resolution under flow.

Lab on a chip·2026
Same journal

Correction to 'scSuperAnnotator: A platform for benchmarking comparison and visualizing automated cellular annotation methods for scRNA-seq data'.

Nucleic acids research·2026
Same journal

Correction to 'Differentiable partition function calculation for RNA'.

Nucleic acids research·2026
Same journal

Deployment of non-canonical splicing in tunicate genomes is mediated by divergent U2AF function and changing m6A modification in U1 and U6 snRNA.

Nucleic acids research·2026
Same journal

Bacillus subtilis DnaB forms multiple protein-protein interactions essential for DNA replication initiation.

Nucleic acids research·2026
Same journal

Multiple forms of protein-protein and DNA binding are exhibited by BrxC from the BREX phage restriction system.

Nucleic acids research·2026
Same journal

Biosynthesis of glycosylated 5-hydroxycytosine in the DNA of diverse viruses.

Nucleic acids research·2026
See all related articles

Related Experiment Video

Updated: May 11, 2026

Novel Sequence Discovery by Subtractive Genomics
09:40

Novel Sequence Discovery by Subtractive Genomics

Published on: January 25, 2019

Reprever: resolving low-copy duplicated sequences using template driven assembly.

Sangwoo Kim1, Paul Medvedev, Tara A Paton

  • 1Department of Computer Science and Engineering, 9500 Gilman Dr University of California at San Diego, La Jolla, CA 92122, USA. sak042@cs.ucsd.edu

Nucleic Acids Research
|May 10, 2013
PubMed
Summary
This summary is machine-generated.

Reprever identifies novel duplicated sequences and their insertion points in genomes. This tool accurately reconstructs duplicon sequences, advancing structural variation discovery and understanding genome evolution.

More Related Videos

Automated Robotic Liquid Handling Assembly of Modular DNA Devices
11:22

Automated Robotic Liquid Handling Assembly of Modular DNA Devices

Published on: December 1, 2017

Related Experiment Videos

Last Updated: May 11, 2026

Novel Sequence Discovery by Subtractive Genomics
09:40

Novel Sequence Discovery by Subtractive Genomics

Published on: January 25, 2019

Automated Robotic Liquid Handling Assembly of Modular DNA Devices
11:22

Automated Robotic Liquid Handling Assembly of Modular DNA Devices

Published on: December 1, 2017

Area of Science:

  • Genomics
  • Evolutionary Biology
  • Bioinformatics

Background:

  • Genomic sequence duplication drives genome evolution and can cause significant variations linked to disease.
  • Discovering novel duplicated sequences, especially using paired-end sequencing, remains a challenge.

Purpose of the Study:

  • To develop and validate a computational tool, Reprever, for identifying and reconstructing novel duplicated sequences (duplicons) and their insertion breakpoints.
  • To improve the discovery of structural variations arising from genomic duplications.

Main Methods:

  • Reprever analyzes paired-end mapped reads and candidate high-copy regions to pinpoint insertion breakpoints.
  • It resolves ambiguous mapping signatures by leveraging profile hidden Markov model (PHMM)-based guided assembly to reconstruct duplicon sequences.

Main Results:

  • Reprever achieved up to 97% accuracy in identifying novel duplicates in simulated genomes with minimal positional and sequence errors.
  • Validation on fosmid sequences and reanalysis of human genomic data (NA18507) identified over 800 novel duplicates, including gene insertions.

Conclusions:

  • Reprever effectively identifies and reconstructs novel duplicated sequences and their insertion sites, overcoming limitations of existing methods.
  • The tool enhances the study of genome evolution and the discovery of structural variations with potential disease implications.