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Genome Annotation and Assembly

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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.
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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.
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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.
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Updated: Apr 23, 2026

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VibrioBase: a model for next-generation genome and annotation database development.

Siew Woh Choo1, Hamed Heydari2, Tze King Tan1

  • 1Department of Oral Biology and Biomedical Sciences, Faculty of Dentistry, University of Malaya, 50603 Kuala Lumpur, Malaysia ; Genome Informatics Research Laboratory, HIR Building, University of Malaya, 50603 Kuala Lumpur, Malaysia.

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Summary

VibrioBase is a new platform offering genomic data and analysis tools for Vibrio research. It aids comparative genomics and pathogenomics, making complex data accessible to researchers.

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Area of Science:

  • Microbiology
  • Genomics
  • Bioinformatics

Background:

  • Increasing volume of Vibrio spp. genomic data requires a dedicated platform.
  • Existing resources may lack specialized analysis tools for Vibrio research.

Purpose of the Study:

  • To introduce VibrioBase, a comprehensive platform for Vibrio genomic data and analysis.
  • To provide researchers with user-friendly tools for comparative genomics and pathogenomics.

Main Methods:

  • Development of a user-friendly sequence database.
  • Integration of standard bioinformatics tools (e.g., BLAST, JBrowse).
  • In-house development of novel tools: Pairwise Genome Comparison (PGC) and Pathogenomics Profiling (PathoProT).

Main Results:

  • VibrioBase hosts 252 Vibrio genomes.
  • Includes general browsing, BLAST, and JBrowse functionalities.
  • PGC and PathoProT tools facilitate easy comparative genomic and pathogenomic analyses.

Conclusions:

  • VibrioBase is a valuable resource for the Vibrio research community.
  • The platform simplifies the analysis of Vibrio genomic data, even for users with limited bioinformatics experience.
  • It supports next-generation database development for microbial genomics.