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

18.4K
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...
18.4K
Non-LTR Retrotransposons03:18

Non-LTR Retrotransposons

12.9K
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...
12.9K
Single Nucleotide Polymorphisms-SNPs01:05

Single Nucleotide Polymorphisms-SNPs

17.6K
A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...
17.6K

You might also read

Related Articles

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

Sort by
Same author

Assessing Genetic Divergence and Adaptive Potential of Aroeira (<i>Myracrodruon urundeuva</i> Allemão LC, Anacardiaceae) Across Brazilian Biomes.

Plants (Basel, Switzerland)·2026
Same author

MCHelper automatically curates transposable element libraries across eukaryotic species.

Genome research·2024
Same author

De novo genome assemblies of two cryptodiran turtles with ZZ/ZW and XX/XY sex chromosomes provide insights into patterns of genome reshuffling and uncover novel 3D genome folding in amniotes.

Genome research·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

The evolutionary history of three Baracoffea species from western Madagascar revealed by chloroplast and nuclear genomes.

PloS one·2024
Same author

Genomic object detection: An improved approach for transposable elements detection and classification using convolutional neural networks.

PloS one·2023

Related Experiment Video

Updated: Dec 9, 2025

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER
14:06

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

Published on: June 23, 2012

15.6K

TIP_finder: An HPC Software to Detect Transposable Element Insertion Polymorphisms in Large Genomic Datasets.

Simon Orozco-Arias1,2, Nicolas Tobon-Orozco1, Johan S Piña1

  • 1Department of Computer Science, Universidad Autónoma de Manizales, Manizales 170002, Colombia.

Biology
|September 12, 2020
PubMed
Summary

Transposable elements (TEs) can alter genomes, causing beneficial or harmful mutations. A new tool, TIP_finder, efficiently detects these mobile element insertions in large genomes using high-performance computing.

Keywords:
HERVHPCTIP_finderTIPsbioinformaticsparallel programmingpolymorphismpost genomic era

More Related Videos

A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes
09:10

A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes

Published on: May 22, 2018

9.6K
Identification of Sleeping Beauty Transposon Insertions in Solid Tumors using Linker-mediated PCR
10:34

Identification of Sleeping Beauty Transposon Insertions in Solid Tumors using Linker-mediated PCR

Published on: February 1, 2013

14.5K

Related Experiment Videos

Last Updated: Dec 9, 2025

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER
14:06

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

Published on: June 23, 2012

15.6K
A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes
09:10

A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes

Published on: May 22, 2018

9.6K
Identification of Sleeping Beauty Transposon Insertions in Solid Tumors using Linker-mediated PCR
10:34

Identification of Sleeping Beauty Transposon Insertions in Solid Tumors using Linker-mediated PCR

Published on: February 1, 2013

14.5K

Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Transposable elements (TEs) are mobile genetic units influencing genome evolution and function.
  • Insertions of TEs, such as LTR-retrotransposons (nearly 8% of the human genome), can lead to beneficial mutations or deleterious effects like cancer.
  • Existing tools struggle with analyzing large genomes and datasets for transposon insertion polymorphisms (TIPs).

Purpose of the Study:

  • To develop an efficient computational tool for detecting mobile element insertions in large genomes.
  • To address the limitations of existing tools in terms of speed and scalability for large-scale genomic analyses.
  • To provide a validated strategy for identifying TIPs in the post-genomic era.

Main Methods:

  • Development of TIP_finder, a computational tool utilizing high-performance computing (HPC) and parallel programming.
  • Inference of discordant read pair analysis using short paired reads (e.g., Illumina), a reference genome, and a TE consensus database.
  • Implementation of an HPC strategy to enhance scalability and reduce analysis runtime.

Main Results:

  • TIP_finder demonstrates significant acceleration in TIP detection, up to 55 times faster in breast cancer datasets and 46 times faster in cancer-free datasets compared to existing algorithms.
  • The tool efficiently analyzes very large genomes and large datasets.
  • The HPC approach ensures scalability for massive genomic data analysis.

Conclusions:

  • TIP_finder provides a validated and accelerated method for detecting transposon insertion polymorphisms.
  • The tool overcomes runtime limitations for large-scale genomic analyses in the post-genomic era.
  • TIP_finder is a valuable resource for researchers studying TEs and their impact on genomes.