CAVES

CAVES compares epitope prediction outputs and Immune Epitope Database (IEDB) search results to identify exact, partial, and novel epitope matches for comparative analyses of putative epitopes among closely related pathogens.

Key Features:

• Two-level analysis framework: Implements a Level-one (L1) and Level-two (L2) analysis approach for structured comparative epitope evaluation.
• Level-one (L1) Analysis: Compares two epitope prediction files to identify similarities and differences between predicted epitopes.
• Level-two (L2) Analysis: Integrates IEDB search results containing experimentally confirmed epitopes to augment comparative findings.
• Match categorization: Classifies epitopes as exact matches, partial matches, or novel epitopes based on degree of peptide matching between datasets.
• Positional sequence data: Utilizes positional sequence information to increase matching accuracy and computational speed.
• Putative epitope comparison: Focuses on intra-species and closely related pathogen comparisons of predicted epitopes to support antigenic analyses.

Scientific Applications:

• Comparative epitope analysis: Detects conserved and divergent epitopes among closely related pathogen sequences.
• Evolutionary and antigenic studies: Supports analysis of antigenic variation and evolutionary relationships between variants.
• Vaccine and therapeutic design: Informs selection of candidate epitopes by identifying experimentally validated and novel epitope matches.
• SARS-CoV-2 variant analysis: Applies to comparative analyses of SARS-CoV-2 variants of concern and their putative epitopes.

Methodology:

Performs L1 comparison of two epitope prediction files to categorize matches as exact, partial, or novel; incorporates IEDB search results in L2 to identify experimentally confirmed epitopes; and uses positional sequence data to improve accuracy and speed.