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Updated: May 10, 2026

Quantification, Viability Assessment, and Visualization Strategies for Acinetobacter Biofilms
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Quantification, Viability Assessment, and Visualization Strategies for Acinetobacter Biofilms

Published on: August 4, 2023

Clustering acinetobacter strains by optical mapping.

Barry G Hall1, Benjamin C Kirkup, Mathew C Riley

  • 1Bellingham Research Institute, Bellingham, Washington, USA.

Genome Biology and Evolution
|June 7, 2013
PubMed
Summary
This summary is machine-generated.

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A new BOP method for optical mapping accurately analyzes bacterial genomes, enabling precise strain typing and clustering. This technique resolves 125 Acinetobacter strains, improving DNA sequence analysis rigor.

Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Optical mapping generates ordered restriction maps of chromosomes.
  • Comparing experimental and in silico optical maps can identify DNA sequence variations.

Purpose of the Study:

  • To introduce the BOP method for comparing optical maps and inferring DNA sequence presence/absence.
  • To develop a computational tool (Optical Mapping suite) for analyzing optical map data.
  • To apply the method for reliable strain typing and clustering of bacterial genomes.

Main Methods:

  • Developed the BOP method and Optical Mapping suite of four programs.
  • Compared experimental optical maps with in silico maps of 125 Acinetobacter strains.
  • Utilized signal-to-noise analysis to assess fragment identification accuracy.
Keywords:
epidemiologygenome alignmentoptical mapping

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Last Updated: May 10, 2026

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  • Employed minimum spanning trees for cluster analysis.

    • Main Results:

    • The BOP method successfully resolved all 125 Acinetobacter strains.
    • Initial analysis misidentified approximately 1/3 of experimental fragments.
    • Clustering reduced misidentification to 3.5%, dividing genomes into three distinct groups.
    • Two clusters contained sequenced genomes, analyzed further with minimum spanning trees.

    Conclusions:

    • The Optical Mapping suite provides a rigorous approach for analyzing optical map data.
    • The BOP method circumvents the need for whole-genome multiple alignments.
    • This technique enables reliable strain typing and clustering based on optical maps.