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

18.8K
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...
18.8K
LTR Retrotransposons03:08

LTR Retrotransposons

19.4K
LTR retrotransposons are class I transposable elements with long terminal repeats flanking an internal coding region. These elements are less abundant in mammals compared to other class I transposable elements. About 8 percent of human genomic DNA comprises LTR retrotransposons. Some of the common examples of LTR retrotransposons are Ty elements in yeast and Copia elements in Drosophila.
The internal coding region of LTR retrotransposons and their mechanism of transposition closely resembles a...
19.4K
DNA-only Transposons02:57

DNA-only Transposons

17.1K
DNA-only transposons are called autonomous transposons since they code for the enzyme transposase that is required for the transposition mechanism. Insertion of transposons can alter gene functions in multiple ways. They can mutate the gene, alter gene expression by introducing a novel promoter or insulator sequence, introduce new splice sites, and change the mRNA transcripts produced, or remodel chromatin structure.
The donor site from where the transposon is excised is either degraded or...
17.1K
Cis-regulatory Sequences02:02

Cis-regulatory Sequences

11.6K
Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
11.6K
Cis-regulatory Sequences02:02

Cis-regulatory Sequences

4.0K
4.0K
Non-LTR Retrotransposons03:18

Non-LTR Retrotransposons

13.1K
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...
13.1K

You might also read

Related Articles

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

Sort by
Same author

The Rlign algorithm for enhanced electrocardiogram analysis through heart rate-corrected ECG alignment for explainable classification and clustering.

European heart journal. Digital health·2026
Same author

Response to 'promising advances and remaining challenges in AI-driven QTc estimation' by Zekai Yu.

Europace : European pacing, arrhythmias, and cardiac electrophysiology : journal of the working groups on cardiac pacing, arrhythmias, and cardiac cellular electrophysiology of the European Society of Cardiology·2026
Same author

Variable partition of non-homogeneous ooplasm sets the stage for divergent potency of 2-cell stage blastomeres.

Molecular human reproduction·2026
Same author

End-to-End Platform for Electrocardiogram Analysis and Model Fine-Tuning: Development and Validation Study.

Journal of medical Internet research·2026
Same author

Catch-Up Weight Gain and Gut Microbiota Development in Full-Term Small for Gestational Age Children During the First Year of Life-A Prospective Cohort Study.

American journal of human biology : the official journal of the Human Biology Council·2026
Same author

Recombination landscape shaped by inversion polymorphisms: a high-density linkage map and chromosome-level assembly of inversion-rich spruce bark beetle genome.

G3 (Bethesda, Md.)·2026
Same journal

Spatial Heterogeneity of Phytoplankton Taxa and Functional Groups Under Multidimensional Environmental Factors in Karst Urban Rivers.

Biology·2026
Same journal

Paleopathology of a Lower Miocene Carettochelyid Turtle from the Moghra Formation, Egypt.

Biology·2026
Same journal

Effects of Type I Diabetes Mellitus and Masticatory Loading on Mandibular Growth in Growing Rats: A Longitudinal CBCT Study.

Biology·2026
Same journal

Data-Limited Stock Status Assessment of Bonga Shad, <i>Ethmalosa fimbriata</i> (Bowdich, 1825) and Lesser African Threadfin, <i>Galeoides decadactylus</i> (Bloch, 1795) in the Central Gulf of Guinea.

Biology·2026
Same journal

Gonadogenesis in the Bearded Dragon (<i>Pogona vitticeps</i>, Agamidae): A Comprehensive Histological Analysis from Gonadal Ridge Formation to Testicular and Ovarian Development.

Biology·2026
Same journal

The Programmable Microbiome: Integrative AI and Multi-Omics Frameworks for Precision T2DM Management.

Biology·2026
See all related articles

Related Experiment Video

Updated: Jan 13, 2026

Real-Time Quantification of the Effects of IS200/IS605 Family-Associated TnpB on Transposon Activity
04:04

Real-Time Quantification of the Effects of IS200/IS605 Family-Associated TnpB on Transposon Activity

Published on: January 20, 2023

2.8K

Transformer-Based Classification of Transposable Element Consensus Sequences with TEclass2.

Lucas Bickmann1, Matias Rodriguez2, Xiaoyi Jiang1

  • 1Department of Computer Science, University of Münster, 48149 Münster, Germany.

Biology
|January 10, 2026
PubMed
Summary
This summary is machine-generated.

Transposable elements (TEs) are key to genome evolution but hard to classify. New software, TEclass2, uses deep learning for accurate TE classification, aiding genomic research.

Keywords:
TE classificationbioinformatics web tooldeep learningtransformer architecturetransposable elements

More Related Videos

Genome-wide Surveillance of Transcription Errors in Eukaryotic Organisms
09:30

Genome-wide Surveillance of Transcription Errors in Eukaryotic Organisms

Published on: September 13, 2018

9.9K
Transposon-insertion Sequencing as a Tool to Elucidate Bacterial Colonization Factors in a Burkholderia gladioli Symbiont of Lagria villosa Beetles
09:55

Transposon-insertion Sequencing as a Tool to Elucidate Bacterial Colonization Factors in a Burkholderia gladioli Symbiont of Lagria villosa Beetles

Published on: August 12, 2021

4.2K

Related Experiment Videos

Last Updated: Jan 13, 2026

Real-Time Quantification of the Effects of IS200/IS605 Family-Associated TnpB on Transposon Activity
04:04

Real-Time Quantification of the Effects of IS200/IS605 Family-Associated TnpB on Transposon Activity

Published on: January 20, 2023

2.8K
Genome-wide Surveillance of Transcription Errors in Eukaryotic Organisms
09:30

Genome-wide Surveillance of Transcription Errors in Eukaryotic Organisms

Published on: September 13, 2018

9.9K
Transposon-insertion Sequencing as a Tool to Elucidate Bacterial Colonization Factors in a Burkholderia gladioli Symbiont of Lagria villosa Beetles
09:55

Transposon-insertion Sequencing as a Tool to Elucidate Bacterial Colonization Factors in a Burkholderia gladioli Symbiont of Lagria villosa Beetles

Published on: August 12, 2021

4.2K

Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Transposable elements (TEs) are abundant in eukaryotic genomes and critical for genome evolution.
  • The complex nature of TE sequences challenges accurate classification and genomic analysis.
  • Current TE classification tools exhibit limitations in reliability and scope.

Purpose of the Study:

  • To develop a novel, accurate, and reliable software tool for classifying transposable element (TE) consensus sequences.
  • To improve the efficiency and accuracy of genomic annotation by addressing challenges in TE identification.
  • To provide a flexible platform for TE classification adaptable to custom datasets.

Main Methods:

  • Developed TEclass2, a software tool utilizing a deep learning approach.
  • Employed a linear transformer architecture with k-mer tokenization and sequence-specific adaptations.
  • Implemented flexible model training capabilities for custom TE datasets.

Main Results:

  • TEclass2 achieved improved classification performance for TE consensus sequences into sixteen superfamilies.
  • The software demonstrated enhanced reliability compared to existing TE classification tools.
  • A web interface with pre-trained models was made available for rapid TE classification.

Conclusions:

  • TEclass2 offers a significant advancement in the accurate and rapid classification of transposable elements.
  • The tool enhances genomic annotation accuracy and supports further bioinformatics research.
  • TEclass2 provides a robust solution for analyzing the complex landscape of TEs in eukaryotic genomes.