VCF2Prot

VCF2Prot converts consequence-called Variant Call Format (VCF) files into sample-specific protein sequences in FASTA format to enable proteogenomics analyses including neo-antigen identification and personalized cancer vaccine development.

Key Features:

• Sequence Intermediate Representation (SIR) algorithm: The SIR algorithm maps consequence-called VCF variant annotations to their corresponding protein sequences using a reference proteome.
• Input and output formats: Accepts consequence-called VCF files and a reference proteome as input and generates sample-specific FASTA protein sequence files as output.
• Performance efficiency: Benchmarking reported approximately 1000-fold faster runtime versus PrecisionProDB, processing 99,254 variants across 8,192 patients in about 11 minutes.
• Parallel and concurrent processing: Implemented with parallel and concurrent programming to support high-throughput genomic datasets.

Scientific Applications:

• Neo-antigen discovery: Generating personalized protein sequences enables identification of tumor-specific neo-antigens.
• Cancer vaccine development: Provides precise variant-derived proteomic sequences to support personalized cancer vaccine target selection.
• Proteogenomics: Bridges genomic variant data and proteomic sequence resources to enable proteogenomic analyses.
• Personalized medicine: Facilitates analyses linking individual genomic variation to proteomic profiles for personalized medicine applications.

Methodology:

VCF2Prot parses consequence-called VCF files and a reference proteome, applies the SIR algorithm to map genomic alterations to protein sequences, and outputs sample-specific FASTA files using parallel and concurrent processing.