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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.
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The double-stranded structure of DNA has two major advantages. First, it serves as a safe repository of genetic information where one strand serves as the back-up in case the other strand is damaged. Second, the double-helical structure can be wrapped around proteins called histones to form nucleosomes, which can then be tightly wound to form chromosomes. This way, DNA chains up to 2 inches long can be contained within microscopic structures in a cell. A double-stranded break not only damages...
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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...
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Gene families consist of groups of genes proposed to have originated from a common ancestor. Typically these arise through events in which a gene or genes are mistakenly duplicated during cell division. Unlike their parent genes (which are subject to selection pressure to maintain function), these gene copies do not need to preserve their sequences and may evolve at a relatively faster rate.
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On Computing Breakpoint Distances for Genomes with Duplicate Genes.

Mingfu Shao1,2, Bernard M E Moret1

  • 11 Laboratory for Computational Biology and Bioinformatics, School of Computer and Communication Sciences , École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland .

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology
|October 28, 2016
PubMed
Summary
This summary is machine-generated.

This study presents fast, exact algorithms for computing breakpoint distances between genomes with duplicate genes. The new "any matching" method significantly improves accuracy in orthology assignment compared to existing tools.

Keywords:
ILPbreakpoint distanceexemplargene familyintermediatemaximum matchingorthology assignment

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Area of Science:

  • Comparative genomics
  • Bioinformatics
  • Computational biology

Background:

  • Calculating genomic distance is crucial for understanding genome organization.
  • Duplicate genes complicate distance calculations, making them NP-hard.
  • Breakpoint distance is a key measure due to its simplicity and model-free nature.

Purpose of the Study:

  • To develop efficient algorithms for breakpoint distance calculation in genomes with duplicate genes.
  • To address the computational challenges of the 'maximum matching' and 'any matching' formulations.
  • To improve orthology assignment accuracy and coverage.

Main Methods:

  • Developed novel exact algorithms based on compact integer-linear programming.
  • Simplified the integer-linear program using variable removal techniques.
  • Validated algorithms using simulations and real biological datasets, including mammalian genomes.

Main Results:

  • Algorithms achieve very fast computation times (seconds) on large genomes.
  • The 'any matching' algorithm significantly outperforms existing methods in accuracy for orthology assignment.
  • The proposed methods demonstrate excellent scalability and achieve near-maximum coverage.

Conclusions:

  • The new algorithms provide efficient and accurate solutions for breakpoint distance computation.
  • This work advances comparative genomics by enabling more precise analysis of genomes with complex structures.
  • The 'any matching' approach offers a superior method for orthology assignment in bioinformatics.