VAPPER

VAPPER profiles variant surface glycoprotein (VSG) repertoires from genomic and transcriptomic sequencing data of Trypanosoma congolense and Trypanosoma vivax to characterize antigenic variation at population scale.

Key Features:

• Automated VSG profiling: Provides an automated approach to profile variant surface glycoprotein (VSG) repertoires from sequencing data.
• Input data types: Accepts genomic and transcriptomic sequencing data for repertoire reconstruction.
• Variant antigen profiles: Generates detailed variant antigen profiles for individual isolates.
• Comparative analysis: Facilitates comparisons of isolate profiles against a comprehensive database of existing strains.
• Handles repertoire complexity: Addresses high sequence variability, copy number variation, and diverse genomic loci characteristic of VSG multi-copy gene families.
• Species focus: Targets livestock pathogens Trypanosoma congolense and Trypanosoma vivax.
• Large-scale methodologies: Implements two distinct yet comparable methodologies for large-scale analysis of variant antigens.
• Implementation: Implemented in Python.

Scientific Applications:

• Population-scale antigenic variation: Characterizes VSG diversity and antigenic variation across parasite populations.
• Comparative genomics: Enables cross-strain comparisons of VSG repertoires to study strain-level variation.
• Transcriptomic repertoire analysis: Profiles expressed VSG repertoires from transcriptomic datasets to study expression-based variation.
• Multi-copy gene family investigation: Supports analysis of complex multi-copy gene families, including copy number and locus diversity effects.
• Vaccine research support: Provides antigen diversity data relevant to vaccine target selection and evaluation.

Methodology:

Automated profiling of VSG repertoires from genomic and transcriptomic sequencing data, generation of detailed variant antigen profiles, and comparative analysis against a database of existing strains using two distinct but comparable large-scale methodologies; implemented in Python.