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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.
Next-generation Sequencing03:00

Next-generation Sequencing

The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features.
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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Related Experiment Video

Updated: May 10, 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

Assembling contigs in draft genomes using reversals and block-interchanges.

Chi-Long Li1, Kun-Tze Chen, Chin Lung Lu

  • 1Department of Computer Science, National Tsing Hua University, Hsinchu 30013, Taiwan. cllu@cs.nthu.edu.tw

BMC Bioinformatics
|June 6, 2013
PubMed
Summary
This summary is machine-generated.

This study presents an efficient algorithm for ordering contigs in draft genomes, improving genome assembly accuracy. The new method outperforms existing tools, especially when genome rearrangements involve transpositions.

More Related Videos

Design and Synthesis of a Reconfigurable DNA Accordion Rack
07:44

Design and Synthesis of a Reconfigurable DNA Accordion Rack

Published on: August 15, 2018

Related Experiment Videos

Last Updated: May 10, 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

Design and Synthesis of a Reconfigurable DNA Accordion Rack
07:44

Design and Synthesis of a Reconfigurable DNA Accordion Rack

Published on: August 15, 2018

Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Next-generation sequencing rapidly produces draft genomes as unassembled contigs.
  • Current algorithms struggle with partially assembled genomes for rearrangement and phylogeny studies.
  • Draft genomes require efficient assembly methods based on reference genomes for applications like resequencing.

Purpose of the Study:

  • To develop an efficient algorithm for the one-sided block ordering problem to assemble draft genomes.
  • To minimize the weighted rearrangement distance between a draft genome and a reference genome.
  • To improve the accuracy of contig assembly in draft genomes.

Main Methods:

  • Developed an algorithm using permutation groups to solve the one-sided block ordering problem.
  • The algorithm calculates weighted rearrangement distance considering reversals and block-interchanges (transpositions) with a 1:2 weight ratio.
  • Implemented the algorithm into a program and compared its performance against a heuristic tool (SIS) using simulated datasets.

Main Results:

  • The algorithm solves the one-sided block ordering problem in O(δn) time, where n is the number of genes/markers and δ is the number of rearrangements.
  • Genome assembly and weighted rearrangement distance calculation are achievable in O(n) time.
  • The implemented program demonstrated superior accuracy compared to the SIS tool, particularly with increased numbers of transpositions.

Conclusions:

  • The developed algorithm provides an efficient and accurate solution for assembling draft genomes using reference genomes.
  • The method is particularly effective in scenarios with significant genomic rearrangements, including transpositions.
  • This work advances computational tools for genome resequencing and comparative genomics.