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OrthoInspector 2.0: Software and database updates.

Benjamin Linard1, Alexis Allot2, Raphaël Schneider2

  • 1LBGI, Computer Science Department, ICube, UMR 7357, University of Strasbourg, CNRS, Fédération de médecine translationnelle, 4 rue Kirschleger 67085 Strasbourg, France and Department of Life Sciences, Natural History Museum, Cromwell Road, London SW7 5BD LBGI, Computer Science Department, ICube, UMR 7357, University of Strasbourg, CNRS, Fédération de médecine translationnelle, 4 rue Kirschleger 67085 Strasbourg, France and Department of Life Sciences, Natural History Museum, Cromwell Road, London SW7 5BD.

Bioinformatics (Oxford, England)
|October 3, 2014
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Summary
This summary is machine-generated.

OrthoInspector now predicts orthology and inparalogy across thousands of proteomes with enhanced visualization tools. Three precomputed orthology databases are now available online for comparative genomics.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • OrthoInspector is a software package for detecting orthology and inparalogy relationships.
  • Previous versions established an original algorithm for these predictions.
  • The package is freely available online with browser support.

Purpose of the Study:

  • To enhance the OrthoInspector package with new functionalities for large-scale orthology prediction.
  • To improve user experience through a refurbished graphical interface and new visualization tools.
  • To provide readily accessible orthology data through online databases.

Main Methods:

  • The original orthology detection algorithm remains unmodified.
  • The package was optimized for predicting orthology across thousands of proteomes.
  • New visualization tools for comparative genomics and protein family analysis were integrated.

Main Results:

  • OrthoInspector now efficiently handles predictions for very large datasets (thousands of proteomes).
  • The graphical interface has been refurbished, and new visualization tools are available.
  • Three online databases of precomputed orthology relationships have been released.

Conclusions:

  • The enhanced OrthoInspector package facilitates large-scale orthology and inparalogy predictions.
  • New features improve comparative genomics and protein family analysis.
  • The release of precomputed databases provides valuable resources for the research community.