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DNA-only Transposons02:57

DNA-only Transposons

14.6K
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...
14.6K
Overview of Transposition and Recombination02:13

Overview of Transposition and Recombination

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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...
15.6K
Transposons01:24

Transposons

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Transposons, or "jumping genes," are small mobile genetic elements (MGEs) that range from 700 to 40,000 base pairs in length. They are found in all organisms and can move within the same chromosome or transfer to different chromosomes. In some cases, transposons can also jump between different host DNA molecules, such as plasmids or viruses, contributing to genetic variability.Barbara McClintock first discovered these mobile genetic elements in the 1940s while studying maize genetics, and she...
52
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...
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LTR Retrotransposons03:08

LTR Retrotransposons

17.6K
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...
17.6K
Horizontal Gene Transfer01:27

Horizontal Gene Transfer

36
Horizontal gene transfer (HGT) is a process where genetic material moves between organisms within the same generation, unlike vertical gene transfer, which occurs from parent to offspring. HGT plays a crucial role in microbial evolution, adaptation, and survival, particularly in shared environments like the human gut.Mobile genetic elements such as plasmids, prophages, integrons, insertion sequences, and transposons facilitate this process. HGT occurs through three primary mechanisms:...
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Related Experiment Video

Updated: Jul 16, 2025

DNA Virus Detection System Based on RPA-CRISPR/Cas12a-SPM and Deep Learning
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Genomic object detection: An improved approach for transposable elements detection and classification using

Simon Orozco-Arias1,2, Luis Humberto Lopez-Murillo1, Johan S Piña1

  • 1Department of Computer Science, Universidad Autónoma de Manizales, Manizales, Colombia.

Plos One
|September 21, 2023
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Summary

A new deep learning method, YORO, accurately detects and classifies transposable elements (TEs) in eukaryotic genomes. This approach uses convolutional neural networks to predict TE position, length, and type, improving genomic analysis efficiency.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Transposable elements (TEs) analysis is vital for understanding eukaryotic genomes.
  • Current TE detection and classification methods are complex and time-consuming.
  • Machine learning (ML) has been applied to TE classification, but not extensively for detection.

Purpose of the Study:

  • To introduce YORO, a novel detection-classification strategy for transposable elements in genomic sequences.
  • To adapt a computer vision convolutional neural network (YOLO) for genomic object detection.
  • To enable prediction of genomic object position, length, and classification in large DNA sequences.

Main Methods:

  • Developed YORO, a strategy based on convolutional neural networks adapted from computer vision.
  • Trained the neural network using internal protein-coding domains of LTR-retrotransposons.
  • Evaluated performance using metrics such as precision, recall, accuracy, F1-score, and execution times.

Main Results:

  • YORO successfully detects and classifies genomic objects, specifically LTR-retrotransposons.
  • The method demonstrates high performance in terms of accuracy and efficiency.
  • Execution times and time ratios indicate significant improvements over existing methods.

Conclusions:

  • YORO represents a promising deep learning approach for the next generation of genomic analysis tools.
  • The strategy enables efficient detection and classification of transposable elements in large DNA sequences.
  • This work facilitates more comprehensive and rapid analysis of eukaryotic genomes.