Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Genome Annotation and Assembly03:36

Genome Annotation and Assembly

18.7K
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.
18.7K
Genomic DNA in Prokaryotes00:46

Genomic DNA in Prokaryotes

43.0K
The genome of most prokaryotic organisms consists of double-stranded DNA organized into one circular chromosome in a region of cytoplasm called the nucleoid. The chromosome is tightly wound, or supercoiled, for efficient storage. Prokaryotes also contain other circular pieces of DNA called plasmids. These plasmids are smaller than the chromosome and often carry genes that confer adaptive functions, such as antibiotic resistance.
Genomic Diversity in Bacteria
Although bacterial genomes are much...
43.0K

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Fluxomics in precision nutrition: integrating dynamic metabolic profiling with multiomics.

Nutrition (Burbank, Los Angeles County, Calif.)·2026
Same author

Identification of High-Performing Blood Metabolite Biomarkers of Lung Cancer in a Chinese Population.

Phenomics (Cham, Switzerland)·2026
Same author

Automated, targeted, NMR spectral profiling of human breast milk.

Metabolomics : Official journal of the Metabolomic Society·2026
Same author

Serum metabolomic profiling reveals LysoPC/PC depletion as a potential biomarker to detect avian reoviral infection in neonatal broiler chickens.

Frontiers in cellular and infection microbiology·2026
Same author

The NMR Exchange Format (NEF): Specification and Applications.

bioRxiv : the preprint server for biology·2026
Same author

A scoring system for validity assessment of biomarkers of food intake.

Critical reviews in food science and nutrition·2026
Same journal

Correction to 'scSuperAnnotator: A platform for benchmarking comparison and visualizing automated cellular annotation methods for scRNA-seq data'.

Nucleic acids research·2026
Same journal

Correction to 'Differentiable partition function calculation for RNA'.

Nucleic acids research·2026
Same journal

Deployment of non-canonical splicing in tunicate genomes is mediated by divergent U2AF function and changing m6A modification in U1 and U6 snRNA.

Nucleic acids research·2026
Same journal

Bacillus subtilis DnaB forms multiple protein-protein interactions essential for DNA replication initiation.

Nucleic acids research·2026
Same journal

Multiple forms of protein-protein and DNA binding are exhibited by BrxC from the BREX phage restriction system.

Nucleic acids research·2026
Same journal

Biosynthesis of glycosylated 5-hydroxycytosine in the DNA of diverse viruses.

Nucleic acids research·2026
See all related articles

Related Experiment Video

Updated: May 9, 2025

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations
08:03

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

Published on: December 7, 2021

2.0K

BASys2: a next-generation bacterial genome annotation system.

Jenna Poelzer1, Scott Han1, Sukanta Saha1

  • 1Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada.

Nucleic Acids Research
|May 1, 2025
PubMed
Summary
This summary is machine-generated.

The Bacterial Annotation System 2.0 (BASys2) significantly accelerates bacterial genome annotation, offering faster and more comprehensive analysis. This advanced system provides enhanced visualization and deeper insights into bacterial genomes and metabolomes.

More Related Videos

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

4.9K
From a Natural Product to Its Biosynthetic Gene Cluster: A Demonstration Using Polyketomycin from Streptomyces diastatochromogenes Tü6028
09:08

From a Natural Product to Its Biosynthetic Gene Cluster: A Demonstration Using Polyketomycin from Streptomyces diastatochromogenes Tü6028

Published on: January 13, 2017

17.1K

Related Experiment Videos

Last Updated: May 9, 2025

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations
08:03

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

Published on: December 7, 2021

2.0K
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

4.9K
From a Natural Product to Its Biosynthetic Gene Cluster: A Demonstration Using Polyketomycin from Streptomyces diastatochromogenes Tü6028
09:08

From a Natural Product to Its Biosynthetic Gene Cluster: A Demonstration Using Polyketomycin from Streptomyces diastatochromogenes Tü6028

Published on: January 13, 2017

17.1K

Area of Science:

  • Microbial genomics
  • Bioinformatics
  • Computational biology

Background:

  • The original Bacterial Annotation System (BASys) was a pioneering web server for bacterial genome annotation since 2005.
  • Advances in web technologies and annotation algorithms necessitate updates to microbial genomics tools.
  • Existing tools may not meet the evolving demands for speed, completeness, and visualization in bacterial genomics.

Purpose of the Study:

  • To develop an upgraded bacterial genome annotation system (BASys2) that incorporates recent technological and algorithmic advancements.
  • To significantly enhance the speed, data output, and visualization capabilities compared to the previous BASys version.
  • To provide researchers with a versatile and powerful tool for in-depth bacterial genome and metabolome analysis.

Main Methods:

  • Developed BASys2, a novel system employing a fast genome-matching and annotation transfer strategy.
  • Integrated over 30 bioinformatics tools and 10 databases for comprehensive annotation.
  • Implemented an interactive genome viewer for dynamic visualization of bacterial genome maps and annotations.
  • Offered multiple access points: web server, desktop application, and Docker image.

Main Results:

  • BASys2 achieves annotation speeds up to 8000× faster than previous systems, reducing annotation time to as little as 10 seconds.
  • The system generates up to 62 annotation fields per gene/protein, doubling the data fields compared to earlier versions.
  • BASys2 supports extensive whole metabolome annotation and complete structural proteome generation.
  • The interactive viewer facilitates dynamic manipulation and detailed inspection of genome data.

Conclusions:

  • BASys2 represents a substantial advancement in bacterial genome annotation, offering unprecedented speed and depth.
  • The system's enhanced visualization and comprehensive annotation capabilities empower microbial genomics research.
  • BASys2 is readily accessible as a web server, desktop viewer, and Docker image, facilitating widespread adoption and use.