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CoreDetector: a flexible and efficient program for core-genome alignment of evolutionary diverse genomes.

Mario Fruzangohar1, Paula Moolhuijzen2, Nicolette Bakaj1

  • 1The Biometry Hub, School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, South Australia 5064, Australia.

Bioinformatics (Oxford, England)
|October 25, 2023
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Summary

CoreDetector efficiently aligns core-genome sequences for eukaryotes, improving flexibility and accuracy over existing tools. This computational method is vital for analyzing sequence variations in diverse species.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Comparative Genomics

Background:

  • Whole genome alignment is crucial for identifying sequence variations and core genomes in eukaryotes.
  • Existing tools struggle with large eukaryotic genomes and divergent species due to computational demands.
  • There is a need for efficient and flexible tools for eukaryotic core-genome analysis.

Purpose of the Study:

  • To introduce CoreDetector, a user-friendly program for aligning core-genome sequences across various genome sizes and divergence levels.
  • To demonstrate the versatility of CoreDetector using fungal, wheat, fly, and rodent genomes.
  • To compare CoreDetector's performance against existing multiple genome alignment tools.

Main Methods:

  • CoreDetector was developed in Java for cross-platform compatibility and easy deployment.
  • A packaged pipeline is executable via bash terminal, requiring no external environments.
  • The tool was tested on diverse datasets, including fungal pathogens, wheat cultivars, and rodent/fly species.

Main Results:

  • CoreDetector successfully aligned core-genome sequences for a range of genome sizes and divergence levels.
  • Alignments of fungal, wheat, fly, and rodent genomes demonstrated CoreDetector's flexibility.
  • CoreDetector showed improved flexibility, efficiency, and competitive accuracy compared to existing tools.

Conclusions:

  • CoreDetector offers an effective solution for eukaryotic core-genome alignment.
  • The tool's ease of use and performance make it valuable for genomic research.
  • CoreDetector provides a flexible and efficient alternative for analyzing sequence and structural variations.