PGM

PGM maps experimentally observed peptides derived from high-throughput mass spectrometry (MS) proteomics data to genomic coordinates to support structural genome annotation.

Key Features:

• Aho-Corasick implementation: Implements the Aho-Corasick string-searching algorithm in Java for efficient exact peptide-to-sequence matching.
• Six-frame translation searches: Searches genomes translated in all six reading frames to identify exact peptide matches.
• Standardized file types: Processes standardized proteomics and sequence file types for input and mapping.
• Genetic code selection: Supports selection of different genetic codes for mapping peptides from diverse organisms.
• Scalability for large genomes: Scales to large eukaryotic genomes to enable genome-wide peptide mapping.

Scientific Applications:

• Proteogenomics: Maps MS-derived peptides to genomic sequences to support proteogenomic analyses.
• Structural genome annotation: Provides peptide-level evidence to inform structural genome annotation.
• Cross-organism annotation: Enables peptide mapping for organisms using different genetic codes.

Methodology:

Implements the Aho-Corasick string-searching algorithm in Java to search standardized file types for exact peptide matches against genomes translated in all six reading frames and supports selection of different genetic codes for mapping peptide locations to the genome.