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Aequatus: an open-source homology browser.

Anil S Thanki1, Nicola Soranzo1, Javier Herrero1,2

  • 1Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK.

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|November 6, 2018
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Summary

Aequatus provides a novel web-based tool for detailed gene structure visualization across gene families. This tool enhances understanding of evolutionary changes by examining gene structure, including ancestral exon boundaries.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Evolutionary Biology

Background:

  • Phylogenetic analysis of homologous genes aids in understanding gene evolution and identifying selection pressures.
  • Gene family and orthogroup characterization is crucial for identifying syntenic blocks.
  • Existing visualization tools offer limited gene-level overviews and lack detail on intra-gene structural changes.

Purpose of the Study:

  • To introduce Aequatus, a web-based tool for in-depth visualization of gene structure across gene families.
  • To address the limitations of current tools in displaying detailed structural changes within genes and conservation of exon boundaries.

Main Methods:

  • Development of Aequatus, an open-source web-based visualization tool.
  • Utilizing precalculated alignment and gene feature data from databases like Ensembl Compara and Core.
  • Offering Aequatus.js, a JavaScript module for visualization, integrated into the Galaxy platform.

Main Results:

  • Aequatus enables detailed examination of gene structure and evolutionary changes within gene families.
  • The tool visualizes conservation of ancestral exon boundaries across multiple genomes.
  • Aequatus.js serves as a plug-in for visualizing gene trees within the Galaxy platform.

Conclusions:

  • Aequatus offers an advanced solution for visualizing gene structure evolution.
  • The tool enhances comparative genomics by providing detailed insights into gene structure conservation.
  • Aequatus facilitates a deeper understanding of evolutionary processes at the gene level.