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Related Concept Videos

Overview of Transposition and Recombination02:13

Overview of Transposition and Recombination

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...
LTR Retrotransposons03:08

LTR Retrotransposons

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...
Transposons01:24

Transposons

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...
Non-LTR Retrotransposons03:18

Non-LTR Retrotransposons

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...
DNA-only Transposons02:57

DNA-only Transposons

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...
Cis-regulatory Sequences02:02

Cis-regulatory Sequences

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...

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Updated: Jun 23, 2026

Use of Alu Element Containing Minigenes to Analyze Circular RNAs
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Analysis of transposable element sequences using CENSOR and RepeatMasker.

Ahsan Huda1, I King Jordan

  • 1School of Biology, Georgia Institute of Technology, Atlanta, GA, USA.

Methods in Molecular Biology (Clifton, N.J.)
|April 21, 2009
PubMed
Summary
This summary is machine-generated.

This study surveys CENSOR and RepeatMasker, key bioinformatics tools for identifying transposable elements (TEs) in eukaryotic genomes. It compares homology-based methods with other approaches for repetitive DNA analysis.

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Related Experiment Videos

Last Updated: Jun 23, 2026

Use of Alu Element Containing Minigenes to Analyze Circular RNAs
13:10

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Determination of the Optimal Chromosomal Location(s) for a DNA Element in Escherichia coli Using a Novel Transposon-mediated Approach
11:12

Determination of the Optimal Chromosomal Location(s) for a DNA Element in Escherichia coli Using a Novel Transposon-mediated Approach

Published on: September 11, 2017

Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Eukaryotic genomes contain substantial repetitive DNA, including transposable elements (TEs).
  • Computational methods are essential for identifying and analyzing these repetitive sequences within large genomic datasets.

Purpose of the Study:

  • To provide a comprehensive survey of two widely used bioinformatics applications, CENSOR and RepeatMasker, for TE detection and analysis.
  • To compare homology-based methods with alternative approaches for repetitive DNA analysis in eukaryotic genomes.

Main Methods:

  • Detailed examination of CENSOR and RepeatMasker, including their availability, input/output formats, and underlying algorithms.
  • Discussion of homology-based, de novo, class-specific, and pipeline methods for repetitive DNA analysis.
  • Illustrative examples of CENSOR and RepeatMasker application.

Main Results:

  • CENSOR and RepeatMasker are readily available tools that utilize homology-based methods for TE detection.
  • Various other methods exist, including de novo, class-specific, and pipeline approaches, each with distinct strengths and weaknesses.
  • These different classes of methods offer complementary utility for comprehensive repetitive DNA analysis.

Conclusions:

  • CENSOR and RepeatMasker are valuable resources for analyzing transposable elements in eukaryotic genomes.
  • Understanding the strengths and limitations of diverse repetitive DNA analysis methods is crucial for effective genomic research.
  • Integrating different analytical strategies enhances the thoroughness of repetitive DNA characterization.