Related Experiment Video
Updated: May 26, 2026
11:58
In-Nucleus Hi-C in Drosophila Cells
Published on: September 15, 2021
Genome dedoubling by DCJ and reversal
Antoine Thomas1, Jean-Stéphane Varré, Aïda Ouangraoua
1LIFL, UMR 8022 CNRS, Université Lille 1, INRIA Lille Nord Europe, Villeneuve d'Ascq, France.
BMC Bioinformatics
|December 14, 2011
Summary
This study introduces the Genome Dedoubling Problem to understand how genome rearrangements cause duplications. Algorithms are developed and applied to reconstruct a non-duplicated ancestor in Drosophila.
Area of Science:
- Genomics
- Computational Biology
- Evolutionary Biology
Background:
- Segmental duplications are a long-standing area of genomic study.
- The breakpoint-duplication phenomenon links segmental duplications to rearrangement breakpoints in mammals and Drosophila.
Purpose of the Study:
- Introduce and analyze the Genome Dedoubling Problem.
- Develop algorithms to find minimum rearrangement scenarios for genome dedoubling.
- Investigate duplications caused by rearrangement breakpoints.
Main Methods:
- Formulate the Genome Dedoubling Problem as a combinatorial challenge.
- Analyze the problem within Double-Cut-and-Join (DCJ) and reversal rearrangement models.
- Develop 2-approximable algorithms for the Genome Dedoubling Problem.
Main Results:
- The Genome Dedoubling Problem is shown to be APX-complete in the DCJ and reversal models.
- Algorithms with 2-approximable guarantees are provided.
- Methods are applied to reconstruct a non-duplicated ancestor of Drosophila yakuba.
Conclusions:
- The Genome Dedoubling Problem and its algorithms are presented.
- Solutions are described for both the DCJ and reversal models.
- The practical utility is demonstrated through analysis of Drosophila data.
Related Concept Videos
01:04¹³C NMR: ¹H–¹³C Decoupling
The probability of having two carbon-13 atoms next to each other is negligible because of the low natural abundance of carbon-13. Consequently, peak splitting due to carbon-carbon spin-spin coupling is not observed in spectra. However, protons up to three sigma bonds away split the carbon signal according to the n+1 rule, resulting in complicated spectra.
A broadband decoupling technique is used to simplify these complex, sometimes overlapping, signals. Broadband decoupling relies on a...
A broadband decoupling technique is used to simplify these complex, sometimes overlapping, signals. Broadband decoupling relies on a...
01:14Diode: Reverse bias
A diode is reverse-biased when the positive terminal of an external voltage source is connected to the n-type material and the negative terminal to the p-type material. This configuration opposes the natural direction of current flow through the diode, effectively increasing the width of the depletion region and the barrier potential. The reverse bias condition produces a minimal leakage current, primarily due to minority charge carriers. This leakage becomes significant when the reverse...
01:24Fast Decoupled and DC Powerflow
The fast decoupled power flow method addresses contingencies in power system operations, such as generator outages or transmission line failures. This method provides quick power flow solutions, essential for real-time system adjustments. Fast decoupled power flow algorithms simplify the Jacobian matrix by neglecting certain elements, leading to two sets of decoupled equations:
01:19DC Generator
An alternator converts mechanical energy into electrical energy that varies sinusoidally, resulting in AC current. Meanwhile, a DC generator converts mechanical energy into electrical energy, which are DC pulses with the same polarity. The construction of a DC generator is similar to that of an alternator, except that the pair of slip rings is replaced by a single split ring, also called a commutator. The commutator functions like a periodic rotary switch; it changes the contacts with the...
01:24Methods of Nuclear Reprogramming
Nuclear reprogramming is a process of transforming one cell type into an unrelated cell type by epigenetic changes that alter the cell’s original gene expression pattern. Such epigenetic changes force cells to express a different set of genes, which play a significant role in inducing transformation into other cell types. Nuclear reprogramming offers applications in reproductive cloning for livestock propagation and regenerative medicine — developing patient-specific cells for injury repair.
02:08Gene Conversion
Other than maintaining genome stability via DNA repair, homologous recombination plays an important role in diversifying the genome. In fact, the recombination of sequences forms the molecular basis of genomic evolution. Random and non-random permutations of genomic sequences create a library of new amalgamated sequences. These newly formed genomes can determine the fitness and survival of cells. In bacteria, homologous and non-homologous types of recombination lead to the evolution of new...