Epitope-Evaluator

Epitope-Evaluator analyzes predicted T-cell epitopes from protein amino acid sequences to characterize epitope distribution, promiscuity, conservation, density, and positional localization across major histocompatibility complex (MHC) alleles for immunological studies.

Key Features:

• Six analysis modules: Provides six distinct tools to analyze predicted T-cell epitopes across MHC alleles.
• Epitope metrics: Quantifies epitope distribution, promiscuity, conservation, density, and location within antigen sequences.
• Customizable parameters: Allows adjustment of cutoffs and analysis parameters for tailored epitope selection and filtering.
• Input format support: Accepts protein sequences in FASTA format and prediction output files from any T-cell epitope predictor.
• Data outputs: Produces plots and tables that can be exported as JPG images and text files.

Scientific Applications:

• Candidate epitope selection: Facilitates identification of candidate T-cell epitopes for experimental validation.
• Allele-specific profiling: Enables comparative profiling across MHC alleles, exemplified by findings that HLA-B*40, HLA-B*27:05, and HLA-B*07:02 recognize fewer epitopes from the SARS-CoV-2 proteome.
• Variant epitope comparison: Identifies shared and variant-specific epitopes among SARS-CoV-2 spike protein variants such as Delta, Omicron, and Wuhan.
• Translational research support: Supports analyses relevant to vaccine design, disease modeling, and personalized medicine.

Methodology:

Implemented using the Shiny/R framework; accepts FASTA protein sequences and epitope prediction outputs, processes these inputs to compute distribution, promiscuity, conservation, density, and positional metrics, and generates visualizations and statistical summaries.