ProteoDisco

ProteoDisco facilitates proteogenomics studies by generating customized protein databases from genomic variants, splice-junctions, fusion genes, and manual transcript sequences.

Key Features:

• Variant Protein Database Generation: Creates customized protein databases incorporating user-submitted genomic variants into protein variant sequences.
• Flexible Input Support: Processes genomic variants, splice-junctions, fusion genes, and manual transcript sequences from standardized formats.
• Cross-Species Compatibility: Functions on all organisms for which a reference genome and transcript annotations are available.
• Modular Workflow: Provides a step-by-step workflow allowing in-depth customization for diverse proteogenomics research approaches.

Scientific Applications:

• Proteogenomics Studies: Enables extended search space identification of novel and variant proteins through customized protein database generation.
• Fusion Gene Analysis: Incorporates fusion gene sequences into protein databases for detecting fusion-derived peptides.
• Alternative Splicing Investigation: Uses splice-junction data to identify proteins resulting from aberrant or alternative splicing events.

Methodology:

ProteoDisco uses an R-based implementation to incorporate genomic variants, fusion genes, and aberrant transcriptomic variants from standardized formats into protein variant sequences.