Title
Epitope-Evaluator: An interactive web application to study predicted T-cell epitopes
Date Issued
01 August 2022
Access level
open access
Resource Type
journal article
Author(s)
Publisher(s)
Public Library of Science
Abstract
Multiple immunoinformatic tools have been developed to predict T-cell epitopes from protein amino acid sequences for different major histocompatibility complex (MHC) alleles. These prediction tools output hundreds of potential peptide candidates which require further processing; however, these tools are either not graphical or not friendly for non-programming users. We present Epitope-Evaluator, a web tool developed in the Shiny/R framework to interactively analyze predicted T-cell epitopes. Epitope-Evaluator contains six tools providing the distribution of epitopes across a selected set of MHC alleles, the promiscuity and conservation of epitopes, and their density and location within antigens. Epitope-Evaluator requires as input the fasta file of protein sequences and the output prediction file coming out from any predictor. By choosing different cutoffs and parameters, users can produce several interactive plots and tables that can be downloaded as JPG and text files, respectively. Using Epitope-Evaluator, we found the HLA-B*40, HLA-B*27:05 and HLA-B*07:02 recognized fewer epitopes from the SARS-CoV-2 proteome than other MHC Class I alleles. We also identified shared epitopes between Delta, Omicron, and Wuhan Spike variants as well as variant-specific epitopes. In summary, Epitope-Evaluator removes the programming barrier and provides intuitive tools, allowing a straightforward interpretation and graphical representations that facilitate the selection of candidate epitopes for experimental evaluation. The web server Epitope-Evaluator is available at https://fuxmanlab.shinyapps.io/EpitopeEvaluator/
Volume
17
Issue
8 August
Language
English
OCDE Knowledge area
Virología
Biofísica
Scopus EID
2-s2.0-85137125502
PubMed ID
Source
PLoS ONE
ISSN of the container
1932-6203
Sponsor(s)
This work was funded by the National Institutes of Health grants R35 GM128625 to J.I.F. B. The funders did not play a role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. The authors would like to thank Manuel Ramirez and Luis Perez for their thoughtful comments during the development of this program.
Sources of information:
Directorio de Producción Científica
Scopus