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

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...

You might also read

Related Articles

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

Sort by
Same author

Molluscivorous red knots rapidly adjust to a plant diet.

Biology open·2026
Same author

Pharmacokinetics of Long-Acting Ampicillin and Its Impact on the Gut Microbiome and Resistome in Rhesus Macaques (Macaca mulatta).

Journal of veterinary pharmacology and therapeutics·2026
Same author

The decline of child stunting in 122 countries: a systematic review of child growth studies since the 19th century.

BMJ global health·2026
Same author

Prophage φEr670 and Genomic Island GI_Er147 as Carriers of Resistance Genes in <i>Erysipelothrix rhusiopathiae</i> Strains.

International journal of molecular sciences·2026
Same author

Targeted isolation of bacteria with potential to competitively exclude Staphylococcus aureus in the upper respiratory tract of pigs.

BMC microbiology·2026
Same author

Bacterial cell-free DNA profiling reveals the co-elevation of multiple bacteria in newborn foals with suspected sepsis.

iScience·2026

Related Experiment Video

Updated: Jul 7, 2026

Competitive Genomic Screens of Barcoded Yeast Libraries
11:59

Competitive Genomic Screens of Barcoded Yeast Libraries

Published on: August 11, 2011

Supervised Lowess normalization of comparative genome hybridization data--application to lactococcal strain

Sacha A F T van Hijum1, Richard J S Baerends, Aldert L Zomer

  • 1Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Kerklaan 30, 9751 NN Haren, The Netherlands. s.a.f.t.van.hijum@rug.nl

BMC Bioinformatics
|February 13, 2008
PubMed
Summary

Supervised Lowess (S-Lowess) improves bacterial genome analysis by accounting for sequence divergence in array-based comparative genome hybridization (aCGH). This method enhances the detection of genomic variations like deletions, outperforming existing normalization techniques.

More Related Videos

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

Detection of Homologous Recombination Intermediates via Proximity Ligation and Quantitative PCR in Saccharomyces cerevisiae
07:55

Detection of Homologous Recombination Intermediates via Proximity Ligation and Quantitative PCR in Saccharomyces cerevisiae

Published on: September 11, 2022

Related Experiment Videos

Last Updated: Jul 7, 2026

Competitive Genomic Screens of Barcoded Yeast Libraries
11:59

Competitive Genomic Screens of Barcoded Yeast Libraries

Published on: August 11, 2011

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

Detection of Homologous Recombination Intermediates via Proximity Ligation and Quantitative PCR in Saccharomyces cerevisiae
07:55

Detection of Homologous Recombination Intermediates via Proximity Ligation and Quantitative PCR in Saccharomyces cerevisiae

Published on: September 11, 2022

Area of Science:

  • Genomics
  • Bioinformatics
  • Microbial genetics

Background:

  • Array-based comparative genome hybridization (aCGH) is standard for bacterial genome analysis.
  • Sequence divergence in prokaryotic genomes complicates accurate detection of genomic variations using aCGH.
  • Existing normalization methods fail to account for sequence divergence, leading to misinterpretation of data.

Purpose of the Study:

  • To develop a novel normalization method for aCGH data that addresses sequence divergence between bacterial strains.
  • To improve the accuracy and sensitivity of detecting genomic variations, such as deletions, in microbial genomes.

Main Methods:

  • Developed Supervised Lowess (S-Lowess), a normalization method utilizing a subset of conserved genes (likely conserved genes, LCG).
  • Implemented a two-step normalization process: 1) identification of LCG, and 2) Lowess normalization using the LCG subset.
  • Assessed S-Lowess performance using aCGH experiments with Lactococcus lactis strains.

Main Results:

  • S-Lowess effectively removes systematic errors from dual-dye aCGH data by normalizing based on conserved genomic regions.
  • In comparative experiments, S-Lowess detected 97% of known deletions in the L. lactis MG1363 genome.
  • Conventional aCGH normalization methods detected a maximum of 60% of these deletions.

Conclusions:

  • S-Lowess significantly outperforms existing normalization methods for microbial aCGH data.
  • The method maximizes the detection of genomic variations, particularly deletions, in bacterial strains.
  • S-Lowess is available as a user-friendly web tool for broader accessibility.