PVS

PVS computes protein sequence variability within multiple sequence alignments (MSAs) to assign absolute site variability scores for epitope identification and structural interpretation.

Key Features:

• Variability Computation: Calculates absolute site variability across MSAs using several predefined metrics.
• Reference Sequence Assignment: Assigns variability scores to a reference sequence chosen as either the first sequence in the alignment or a consensus sequence.
• Visualization and Structural Analysis: Maps and plots site variability onto 3D protein structures to relate sequence variation to structure.
• Epitope Discovery Support: Identifies conserved fragments within MSAs using user-defined variability thresholds to facilitate epitope selection for vaccine design.
• Integration with RANKPEP: Generates a variability-masked sequence for submission to RANKPEP for conserved T-cell epitope prediction.

Scientific Applications:

• Structure-Function Studies: Relates sequence variability to 3D structural data to support analysis of structural implications of substitutions.
• Vaccine Design: Identifies conserved regions within variable proteins to inform epitope-based vaccine development against rapidly evolving pathogens.
• Immunological Research: Supports investigation of immune evasion mechanisms and selection of conserved epitopes for immunological studies.

Methodology:

Computes absolute site variability across MSAs using several predefined metrics, assigns scores to either the first alignment sequence or a consensus sequence, identifies conserved fragments by applying user-defined variability thresholds, generates variability-masked sequences, maps variability onto 3D structures, and outputs sequences for submission to RANKPEP.