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Related Concept Videos

Conservative Site-specific Recombination and Phase Variation02:53

Conservative Site-specific Recombination and Phase Variation

Because the DNA segments are cut and reorganized in a direction-specific manner, site-specific recombination has emerged as an efficient genetic engineering technique. Flippase and Cyclization recombinases or Flp and Cre, respectively, are two members of the tyrosine recombinase family derived from bacteriophages, that are used to mediate site-specific DNA insertions, deletions, and targeted expression of proteins in mammalian cell lines.
The recognition sites for Cre recombinase called LoxP...
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...
Homologous Recombination02:31

Homologous Recombination

The basic reaction of homologous recombination (HR) involves two chromatids that contain DNA sequences sharing a significant stretch of identity. One of these sequences uses a strand from another as a template to synthesize DNA in an enzyme-catalyzed reaction. The final product is a novel amalgamation of the two substrates. To ensure an accurate recombination of sequences, HR is restricted to the S and G2 phases of the cell cycle. At these stages, the DNA has been replicated already and the...
Homologous Recombination02:31

Homologous Recombination

The basic reaction of homologous recombination (HR) involves two chromatids that contain DNA sequences sharing a significant stretch of identity. One of these sequences uses a strand from another as a template to synthesize DNA in an enzyme-catalyzed reaction. The final product is a novel amalgamation of the two substrates. To ensure an accurate recombination of sequences, HR is restricted to the S and G2 phases of the cell cycle. At these stages, the DNA has been replicated already and the...
Exon Recombination02:32

Exon Recombination

The evolution of new genes is critical for speciation. Exon recombination, also known as exon shuffling or domain shuffling, is an important means of new gene formation. It is observed across vertebrates, invertebrates, and in some plants such as potatoes and sunflowers. During exon recombination, exons from the same or different genes recombine and produce new exon-intron combinations, which might evolve into new genes. 
Exon shuffling follows “splice frame rules.” Each exon has three reading...
RACE - Rapid Amplification of cDNA Ends02:35

RACE - Rapid Amplification of cDNA Ends

Rapid Amplification of cDNA Ends, or RACE, is one of the most effective methods to obtain a full-length cDNA from an mRNA sequence between a known internal region to the unknown sequence at the 5’ or 3’ end. The unknown region is cloned in the cDNA by a gene-specific primer that binds the known end, and a hybrid primer that attaches a predefined anchor sequence to the unknown end of the cDNA. The sequence in between is amplified by PCR with an anchor primer and a gene-specific primer.
Since the...

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Related Experiment Video

Updated: Jun 9, 2026

Simultaneous Quantification of T-Cell Receptor Excision Circles (TRECs) and K-Deleting Recombination Excision Circles (KRECs) by Real-time PCR
14:14

Simultaneous Quantification of T-Cell Receptor Excision Circles (TRECs) and K-Deleting Recombination Excision Circles (KRECs) by Real-time PCR

Published on: December 6, 2014

RDP3: a flexible and fast computer program for analyzing recombination.

Darren P Martin1, Philippe Lemey, Martin Lott

  • 1Computational Biology Group, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Centre for High Performance Computing, Rosebank, Cape Town, South Africa. darrenpatrickmartin@gmail.com

Bioinformatics (Oxford, England)
|August 28, 2010
PubMed
Summary
This summary is machine-generated.

RDP3 is a new software version for analyzing DNA sequence recombination. It offers advanced methods, visualization tools, and automated analysis for large datasets, improving recombination event characterization.

More Related Videos

Molecular Evolution of the Tre Recombinase
12:02

Molecular Evolution of the Tre Recombinase

Published on: May 29, 2008

Related Experiment Videos

Last Updated: Jun 9, 2026

Simultaneous Quantification of T-Cell Receptor Excision Circles (TRECs) and K-Deleting Recombination Excision Circles (KRECs) by Real-time PCR
14:14

Simultaneous Quantification of T-Cell Receptor Excision Circles (TRECs) and K-Deleting Recombination Excision Circles (KRECs) by Real-time PCR

Published on: December 6, 2014

Molecular Evolution of the Tre Recombinase
12:02

Molecular Evolution of the Tre Recombinase

Published on: May 29, 2008

Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • The RDP (Recombination Detection Program) is a widely used tool for analyzing DNA sequence recombination.
  • Previous versions have facilitated the identification of recombination events in various biological contexts.

Purpose of the Study:

  • To introduce RDP3, a significantly enhanced version of the RDP program.
  • To provide advanced computational tools for the detailed characterization of recombination events in DNA sequence alignments.

Main Methods:

  • Implementation of four novel recombination analysis methods: 3SEQ, VISRD, PHYLRO, and LDHAT.
  • Development of new tests for identifying recombination hotspots.
  • Integration of matrix methods for visualizing recombination patterns and recombination-aware ancestral sequence reconstruction.
  • Enhancement of the graphical user interface for interactive analysis and cross-checking of results.

Main Results:

  • RDP3 accommodates large datasets, analyzing alignments up to 20 x 2 megabase sequences within 48 hours on a desktop PC.
  • The software offers a high degree of analysis flow automation.
  • New visualization methods aid in the detailed examination of recombination signals.

Conclusions:

  • RDP3 represents a substantial advancement in computational tools for recombination analysis.
  • The enhanced features and scalability of RDP3 facilitate more robust and efficient characterization of recombination events in large genomic datasets.