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Related Concept Videos

Gene Conversion02:08

Gene 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...
Gene Conversion02:08

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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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Base Excision Repair01:54

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One of the common DNA damages is the chemical alteration of single bases by alkylation, oxidation, or deamination. The altered bases cause mispairing and strand breakage during replication. This type of damage causes minimal change to the DNA double helix structure and can be repaired by the base excision repair (BER) pathways. BER corrects damaged DNA sequences by removing the damaged base and restoring the original base sequence using the complementary strand as a template.
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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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Introductory Analysis and Validation of CUT&RUN Sequencing Data
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Double cut and join with insertions and deletions.

Marília D V Braga1, Eyla Willing, Jens Stoye

  • 1Technische Fakultät, Universität Bielefeld, Bielefeld, Germany. mdbraga@inmetro.gov.br

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology
|September 9, 2011
PubMed
Summary
This summary is machine-generated.

This study introduces a novel linear time algorithm for calculating genomic distance between multichromosomal genomes with differing gene content, accounting for insertions, deletions, and double cut and join (DCJ) operations. The method also enables genome sorting and addresses challenges with the triangle inequality, with applications in analyzing Rickettsia species.

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Area of Science:

  • Genomics
  • Computational Biology
  • Evolutionary Biology

Background:

  • Genomic distance calculations are often restricted to genomes with identical content and no duplicated markers.
  • Gene content differences are evolutionarily significant but challenging to model precisely.
  • Existing algorithms for genomic rearrangements, insertions, and deletions typically have polynomial time complexity.

Purpose of the Study:

  • To develop the first linear time algorithm for computing genomic distance between multichromosomal genomes with unequal gene content.
  • To introduce algorithms for genome sorting using double cut and join (DCJ) operations, insertions, and deletions.
  • To analyze the impact of different sorting scenarios and address potential disruptions to the triangle inequality.

Main Methods:

  • Developed a linear time algorithm for genomic distance computation considering unequal gene content, insertions, deletions, and DCJ operations.
  • Derived algorithms for sorting one genome into another under the same operational constraints.
  • Compared sorting scenarios based on maximizing/minimizing DCJ operations relative to insertions/deletions.
  • Investigated and proposed a correction for triangle inequality violations using non-common markers.

Main Results:

  • Achieved a linear time complexity for genomic distance calculation in multichromosomal genomes with unequal content.
  • Provided optimal sorting algorithms that consider DCJ, insertion, and deletion operations.
  • Demonstrated that the triangle inequality can be corrected by adjusting for non-common markers.
  • Identified preliminary evidence of deletion clusters in six Rickettsia species.

Conclusions:

  • The new algorithm significantly advances the computational efficiency of genomic distance analysis for complex genomes.
  • The developed sorting methods offer flexibility in evolutionary and comparative genomics studies.
  • The findings provide a robust framework for analyzing genomic evolution, even with non-standard genomic distances.
  • Application to Rickettsia suggests potential insights into their parasitic evolution and genome dynamics.