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Related Concept Videos

Genome Annotation and Assembly03:36

Genome Annotation and Assembly

The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
Viral Recombination00:57

Viral Recombination

Cells are sometimes infected by more than one virus at once. When two viruses disassemble to expose their genomes for replication in the same cell, similar regions of their genomes can pair together and exchange sequences in a process called recombination. Alternatively, viruses with segmented genomes can swap segments in a process called reassortment.
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...
Homologous Recombination02:31

Homologous Recombination

The basic reaction of homologous recombination (HR) involves two chromatids that contain DNA sequences sharing a significant stretch of identity. One of these sequences uses a strand from another as a template to synthesize DNA in an enzyme-catalyzed reaction. The final product is a novel amalgamation of the two substrates. To ensure an accurate recombination of sequences, HR is restricted to the S and G2 phases of the cell cycle. At these stages, the DNA has been replicated already and the...
Homologous Recombination02:31

Homologous Recombination

The basic reaction of homologous recombination (HR) involves two chromatids that contain DNA sequences sharing a significant stretch of identity. One of these sequences uses a strand from another as a template to synthesize DNA in an enzyme-catalyzed reaction. The final product is a novel amalgamation of the two substrates. To ensure an accurate recombination of sequences, HR is restricted to the S and G2 phases of the cell cycle. At these stages, the DNA has been replicated already and the...
Conservative Site-specific Recombination and Phase Variation02:53

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.
The recognition sites for Cre recombinase called LoxP...

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Updated: May 15, 2026

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies
12:08

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies

Published on: August 20, 2021

Reconstructing genome mixtures from partial adjacencies.

Ahmad Mahmoody1, Crystal L Kahn, Benjamin J Raphael

  • 1Department of Computer Science, Brown University, Providence, RI, USA. ahmad@cs.brown.edu

BMC Bioinformatics
|January 4, 2013
PubMed
Summary
This summary is machine-generated.

Researchers developed the k-minimum completion problem (k-MCP) to reconstruct cancer genomes from mixed DNA sequencing data. This computational approach aids in identifying somatic mutations driving cancer progression.

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Last Updated: May 15, 2026

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies
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Published on: August 20, 2021

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Published on: July 13, 2013

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08:03

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Area of Science:

  • Computational Biology
  • Genomics
  • Bioinformatics

Background:

  • Cancer genome sequencing aims to identify driver mutations.
  • Tumor heterogeneity complicates mutation analysis due to mixed genomes in sequencing data.
  • Genome rearrangements are key somatic mutations, but their assignment to individual cancer genomes is challenging.

Purpose of the Study:

  • To formulate and analyze the k-minimum completion problem (k-MCP) for reconstructing multiple cancer genomes from mixed sequencing data.
  • To address the challenge of assigning detected rearrangements to specific genomes within a tumor.
  • To provide a computational framework for analyzing complex cancer genome data.

Main Methods:

  • Formulation of the k-minimum completion problem (k-MCP).
  • Algorithmic analysis of k-MCP for different values of k and chromosomal structures.
  • Investigation of computational complexity, including linear time solvability and NP-completeness.

Main Results:

  • The 1-minimum completion problem (1-MCP) is solvable in linear time for single circular or linear chromosomes without restrictions.
  • The k-minimum completion problem (k-MCP) is NP-complete for k ≥ 3 and for k=2 with the double-cut-and-join (DCJ) distance.
  • These findings establish theoretical foundations for k-MCP algorithms.

Conclusions:

  • The k-MCP provides a novel computational framework for reconstructing cancer genomes from mixed sequencing data.
  • The complexity results highlight the computational challenges in reconstructing multiple cancer genomes.
  • This work lays the groundwork for applying k-MCP algorithms to real-world cancer sequencing data analysis.