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

Overview of Transposition and Recombination02:13

Overview of Transposition and Recombination

15.9K
Transposons make up a significant part of genomes of various organisms. Therefore, it is believed that transposition played a major evolutionary role in speciation by changing genome sizes and modifying gene expression patterns. For example, in bacteria, transposition can lead to conferring antibiotic resistance. Movement of transposable elements within the genetic pool of pathogenic bacteria can aid in transfer of antibiotic-resistant genetic elements. In eukaryotes, transposons can carry out...
15.9K
RNA-seq03:21

RNA-seq

10.2K
RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
10.2K
Genome Annotation and Assembly03:36

Genome Annotation and Assembly

19.0K
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.
19.0K
Non-LTR Retrotransposons03:18

Non-LTR Retrotransposons

11.6K
As the name suggests, non-LTR retrotransposons lack the long terminal repeats characteristic of the LTR retrotransposons. Additionally, both LTR and non-LTR retrotransposons use distinct mechanisms of mobilization. Non-LTR retrotransposons are further divided into two classes - Long interspersed nuclear elements (LINEs) and short interspersed nuclear elements (SINEs), both of which occur abundantly in most mammals, including humans. Some of the active non-LTR retrotransposons in humans are L1...
11.6K
Sanger Sequencing01:57

Sanger Sequencing

755.5K
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...
755.5K

You might also read

Related Articles

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

Sort by
Same author

Host-transposable element coexistence: a matter of resistance, tolerance and trade-off.

The EMBO journal·2026
Same author

Transposable elements contribute to the evolution of host shift-related genes in cactophilic <i>Drosophila</i> species.

Genome research·2026
Same author

Why and how to set up a Bioinformatics Learning Lab (BILL).

PLoS computational biology·2025
Same author

Effective population size does not explain long-term variation in genome size and transposable element content in animals.

eLife·2025
Same author

Temporal and spatial niche partitioning in a retrotransposon community of the Drosophila melanogaster genome.

Nucleic acids research·2025
Same author

Two distinct host-specialized fungal species cause white-nose disease in bats.

Nature·2025

Related Experiment Video

Updated: Aug 4, 2025

Genetic Mapping of Thermotolerance Differences Between Species of Saccharomyces Yeast via Genome-Wide Reciprocal Hemizygosity Analysis
10:08

Genetic Mapping of Thermotolerance Differences Between Species of Saccharomyces Yeast via Genome-Wide Reciprocal Hemizygosity Analysis

Published on: August 12, 2019

17.3K

TrEMOLO: accurate transposable element allele frequency estimation using long-read sequencing data combining assembly

Mourdas Mohamed1, François Sabot2,3, Marion Varoqui1

  • 1Institute of Human Genetics, UMR9002, CNRS and Université de Montpellier, Montpellier, France.

Genome Biology
|April 4, 2023
PubMed
Summary

Transposable Element MOnitoring with LOng-reads (TrEMOLO) is a novel software for detecting transposable elements (TEs) and their frequencies in populations. TrEMOLO offers robust performance, outperforming existing tools in analyzing genome assemblies.

Keywords:
GenomeHaplotypesLong-read DNA sequencingNanopore sequencingSoftwareStructural variationTransposable element allelic frequencyTransposable element calling

More Related Videos

Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved Non-model Organisms
10:41

Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved Non-model Organisms

Published on: May 9, 2017

9.3K
Targeted DNA Methylation Analysis by Next-generation Sequencing
08:38

Targeted DNA Methylation Analysis by Next-generation Sequencing

Published on: February 24, 2015

37.2K

Related Experiment Videos

Last Updated: Aug 4, 2025

Genetic Mapping of Thermotolerance Differences Between Species of Saccharomyces Yeast via Genome-Wide Reciprocal Hemizygosity Analysis
10:08

Genetic Mapping of Thermotolerance Differences Between Species of Saccharomyces Yeast via Genome-Wide Reciprocal Hemizygosity Analysis

Published on: August 12, 2019

17.3K
Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved Non-model Organisms
10:41

Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved Non-model Organisms

Published on: May 9, 2017

9.3K
Targeted DNA Methylation Analysis by Next-generation Sequencing
08:38

Targeted DNA Methylation Analysis by Next-generation Sequencing

Published on: February 24, 2015

37.2K

Area of Science:

  • Genomics
  • Bioinformatics
  • Population Genetics

Background:

  • Transposable elements (TEs) are mobile genetic sequences that influence genome evolution.
  • Accurate detection and frequency estimation of TEs are crucial for understanding their dynamics and impact.
  • Existing computational tools have limitations in comprehensively analyzing TE insertions and deletions.

Purpose of the Study:

  • To introduce TrEMOLO, a new software tool for robust transposable element (TE) detection and allele frequency estimation.
  • To evaluate TrEMOLO's performance against existing state-of-the-art methods using simulated and experimental data.
  • To provide a comprehensive tool for studying TE dynamics in various genome qualities.

Main Methods:

  • TrEMOLO combines assembly- and mapping-based approaches for TE detection.
  • The software analyzes both high- and low-quality genome assemblies.
  • Performance benchmarking was conducted using simulated datasets and validated with experimental data.

Main Results:

  • TrEMOLO accurately detects most transposable element insertions and deletions.
  • The software effectively estimates TE allele frequencies in populations.
  • Benchmarking demonstrated that TrEMOLO outperforms other leading computational tools.

Conclusions:

  • TrEMOLO is a comprehensive and accurate tool for studying transposable element dynamics.
  • The software provides reliable TE detection and frequency estimation across different genome assembly qualities.
  • TrEMOLO represents a significant advancement in the computational analysis of transposable elements.