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Related Concept Videos

Comparing Copy Number Variations and SNPs02:26

Comparing 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%...
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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.
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Gene Conversion

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Gene Duplication and Divergence

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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...

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Detection of Rare Mutations in CtDNA Using Next Generation Sequencing
11:11

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Published on: August 24, 2017

Sorting by reversals, block interchanges, tandem duplications, and deletions.

Martin Bader1

  • 1Institute of Theoretical Computer Science, University of Ulm, 89069 Ulm, Germany. martin.bader@uni-ulm.de

BMC Bioinformatics
|February 12, 2009
PubMed
Summary

This study introduces a new heuristic algorithm for genome rearrangement, handling gene duplications and deletions of any size. It effectively sorts ancestral genomes into descendant genomes, providing good approximations of evolutionary distances.

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Area of Science:

  • Comparative genomics
  • Bioinformatics
  • Evolutionary biology

Background:

  • Genome rearrangement is a key problem in comparative genomics.
  • Existing algorithms often assume unique gene content, not reflecting biological reality.
  • Handling unequal gene content, especially duplications and deletions, is challenging.

Purpose of the Study:

  • To develop a heuristic algorithm for sorting ancestral genomes into descendant genomes.
  • To accommodate arbitrary gene content, including duplications and deletions of any size.

Main Methods:

  • Developed a heuristic algorithm for genome sorting.
  • Incorporated reversals, block interchanges, tandem duplications, and deletions.
  • Allowed arbitrary sizes for tandem duplications and deletions.

Main Results:

  • The algorithm successfully sorts ancestral genomes into descendant genomes with arbitrary gene content.
  • It handles tandem duplications and deletions of arbitrary sizes.
  • Sorting sequences found are close to optimal for closely related genomes.

Conclusions:

  • The algorithm provides a good approximation of true evolutionary distances.
  • Performance quality decreases with increased genome divergence or size.
  • This method advances the study of genome evolution with complex gene content.