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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.
Modern Molecular Taxonomy01:29

Modern Molecular Taxonomy

Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
Evolution of Microbial Genome01:08

Evolution of Microbial Genome

Microbial genome evolution is a highly dynamic process shaped by continual gene gain and loss across species and strains. This genomic flexibility allows microorganisms to adapt rapidly to environmental pressures and interactions with other organisms. Central to understanding this diversity is the distinction between the core and pan genomes.The core genome comprises the genes shared by all sampled strains of a species, representing essential functions needed for fundamental cellular processes.
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.
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 18, 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

Improved variation calling via an iterative backbone remapping and local assembly method for bacterial genomes.

Hongseok Tae1, Robert E Settlage, Shamira Shallom

  • 1Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA, USA.

Genomics
|September 13, 2012
PubMed
Summary

ReviSeq improves bacterial genome variant calling, especially for complex regions and long insertions. This new program offers more accurate sequencing data analysis for researchers studying bacterial evolution and disease.

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Amplification, Next-generation Sequencing, and Genomic DNA Mapping of Retroviral Integration Sites

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Area of Science:

  • Genomics
  • Bioinformatics
  • Microbial sequencing

Background:

  • Sequencing data analysis faces challenges with low complexity repeats and transposons due to errors and short reads.
  • Accurate variant identification is crucial for understanding bacterial populations and evolution.

Purpose of the Study:

  • To develop a novel computational tool, ReviSeq, for enhanced bacterial genome variant detection.
  • To improve the accuracy of identifying single nucleotide variants (SNVs) and insertions/deletions (INDELs), particularly long INDELs.

Main Methods:

  • ReviSeq employs a hybrid approach combining iterative remapping and local assembly onto a bacterial sequence backbone.
  • The method was validated using six *Brucella suis* field isolates against a revised reference genome.
  • Performance was compared against established pipelines like STAMPY/SAMtools, BWA/SAMtools, iCORN, and BWA/PINDEL.

Main Results:

  • ReviSeq identified more variants per sample compared to all tested pipelines, including an average of 87 variants (SNVs, short and long INDELs) per strain.
  • The program demonstrated superior performance in calling long INDELs.
  • It also excluded false positive variants identified by other methods.

Conclusions:

  • ReviSeq offers a significant advancement in bacterial genome sequencing data analysis.
  • The tool enhances variant detection accuracy, particularly for challenging genomic regions and complex structural variations.
  • ReviSeq is publicly available for use in microbial genomics research.