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D-GENIES: dot plot large genomes in an interactive, efficient and simple way.

Floréal Cabanettes1, Christophe Klopp1

  • 1Plate-forme bio-informatique Genotoul, Mathématiques et Informatique Appliquées de Toulouse, INRA, Castanet Tolosan, France.

Peerj
|June 12, 2018
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Summary

D-GENIES is a new tool for comparing large genome sequences using interactive dot plots. It overcomes input size limitations of other tools, offering a synthetic overview of sequence similarity.

Keywords:
Dot plotGenome assessmentInteractive user interfaceLarge genomes

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Area of Science:

  • Bioinformatics
  • Genomics
  • Computational Biology

Background:

  • Dot plots are essential for visualizing genomic sequence similarity, aiding in the identification of structural variations like repetitions, breaks, and inversions.
  • Existing dot plot generation tools often struggle with large input sequence sizes, limiting their utility for comprehensive genome comparisons.

Purpose of the Study:

  • To introduce D-GENIES, a novel standalone and web application designed for large-scale genome alignments and interactive dot plot generation.
  • To provide a user-friendly and efficient solution for visualizing genomic similarities, overcoming the limitations of existing tools regarding input sequence size.

Main Methods:

  • D-GENIES utilizes the minimap2 software package for efficient and accurate large genome alignments.
  • The application generates interactive dot plots, allowing users to sort query sequences, zoom into specific regions, and explore sequence relationships.
  • Developed as an open-source package in Python and JavaScript, D-GENIES is designed for easy installation and accessibility.

Main Results:

  • D-GENIES successfully performs large genome alignments and generates interactive dot plots, offering a synthetic overview of sequence similarity.
  • The tool enables users to download various outputs, including image files, alignment data, and sequence files, facilitating further analysis.
  • The interactive nature of the plots allows for detailed exploration of genomic rearrangements and similarities.

Conclusions:

  • D-GENIES provides a robust and scalable solution for generating genomic alignment dot plots, particularly for large sequence datasets.
  • Its interactive features and ease of use make it a valuable tool for researchers in genomics and bioinformatics.
  • The open-source availability and web application further enhance its accessibility and potential for widespread adoption in the scientific community.