Related Experiment Video
Updated: May 22, 2026
06:40
G2-seq: A High Throughput Sequencing-based Technique for Identifying Late Replicating Regions of the Genome
Published on: March 22, 2018
Detecting long tandem duplications in genomic sequences.
Eric Audemard1, Thomas Schiex, Thomas Faraut
1Unité de Biométrie et Intelligence Artificielle, UR 875, INRA, Toulouse, France. Eric.Audemard@gmail.com
BMC Bioinformatics
|May 10, 2012
Summary
ReD Tandem software identifies large tandem duplications directly at the DNA level, complementing traditional methods. This tool aids in understanding genome evolution by detecting novel gene and non-coding element duplications.
Area of Science:
- Genomics
- Bioinformatics
- Evolutionary Biology
Background:
- Genome sequencing provides insights into genome evolution and the emergence of novel functions.
- Traditional gene duplication detection methods, focusing on protein comparisons, offer a limited perspective on evolutionary processes.
Purpose of the Study:
- Introduce ReD Tandem, a novel software for detecting tandem duplication arrays.
- Enable direct DNA-level detection of tandem duplications, including those with weak similarities.
Main Methods:
- Utilize a flow-based chaining algorithm for tandem duplication detection.
- Apply ReD Tandem to the *A. thaliana* genome using a reference set of tandem duplicated genes.
Main Results:
- ReD Tandem effectively predicts a significant fraction of recently duplicated genes (dS < 1).
- The software identifies tandem duplications involving non-coding elements like pseudogenes and RNA genes.
- ReD Tandem performs agnostic identification of tandem duplications without relying on gene annotations.
Conclusions:
- ReD Tandem complements protein-based methods by identifying duplications in non-coding regions.
- The software provides a more comprehensive view of evolutionary processes by recovering overlooked duplication events.
- ReD Tandem has the potential to improve existing genome annotations.
Related Concept Videos
02:37Gene Duplication and Divergence
The seminal work of Ohno in 1970 popularized the idea of gene duplication and divergence. DNA sequence comparison studies reveal that a large portion of the genes in bacteria, archaebacteria, and eukaryotes was generated by gene duplication and divergence, indicating its critical role in evolution.
The duplicated copies of the gene are called Paralogs. Paralogs with similar sequences and functions form a gene family. Across several species, a large number of gene families are characterized.
The duplicated copies of the gene are called Paralogs. Paralogs with similar sequences and functions form a gene family. Across several species, a large number of gene families are characterized.
01:57Sanger Sequencing
DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...
03:00Next-generation Sequencing
The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features.
02:26Comparing Copy Number Variations and SNPs
Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...