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ImmunomeBrowser: a tool to aggregate and visualize complex and heterogeneous epitopes in reference proteins.

Sandeep Kumar Dhanda1, Randi Vita1, Brendan Ha1

  • 1Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA.

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Summary

This study introduces an enhanced ImmunomeBrowser tool for aggregating and visualizing diverse immunological datasets. It helps identify dominant immune response regions within user-provided protein sequences and experimental data.

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Area of Science:

  • Immunology
  • Bioinformatics
  • Computational Biology

Background:

  • Immunological datasets from different studies often exhibit heterogeneity due to variations in experimental methods, peptide testing, and donor numbers.
  • Aggregating and visualizing such diverse data is crucial for identifying key immune epitopes and response patterns.

Purpose of the Study:

  • To present a customized application of the Immune Epitope Database's (IEDB) ImmunomeBrowser tool for handling heterogeneous immunological data.
  • To enable effective aggregation and visualization of user-provided peptide sets and associated response data against a reference protein sequence.

Main Methods:

  • A customized version of the IEDB ImmunomeBrowser was developed to process user-submitted peptide data and response information.
  • The tool maps input data to a user-specified protein reference sequence.
  • Output includes tables and interactive visualizations (Response Frequency score, confidence intervals) generated via a web interface.

Main Results:

  • The application successfully aggregates and visualizes heterogeneous immunological data, including MHC ligand elution and B/T cell epitope screening data.
  • It generates a Response Frequency score and confidence intervals to highlight dominant immune response regions and their boundaries.
  • Results are accessible through an interactive JavaScript web interface and downloadable tabular formats.

Conclusions:

  • The enhanced ImmunomeBrowser provides a powerful platform for analyzing diverse immunological datasets.
  • It facilitates the identification of key epitopes and immune response patterns, aiding further research in immunoinformatics and vaccinology.
  • The tool is freely accessible online, promoting broader use in the scientific community.