WhatsGNU

WhatsGNU identifies proteomic novelty by using exact-match proteomic compression to rapidly classify genomes, quantify allelic novelty with the GNU score, and contextualize individual genomes within large collections for genomic diversity analyses.

Key Features:

• Exact-match proteomic compression: Compresses proteomes by identifying exact-match protein sequences across genomes to reduce redundancy.
• GNU score: Quantifies proteomic novelty by ranking protein sequences based on observed exact matches across known genomes within a species.
• Use of public-database variation: Leverages natural variation present in public databases to contextualize and rank protein sequences.
• Rapid genome classification: Classifies new genomes swiftly by comparing their proteomes to the compressed reference of exact-match proteins.
• Whole-protein and allele reports: Generates comprehensive whole-protein reports that list protein alleles and highlight potential novel functional differences.
• Scalability: Employs computationally scalable methodologies to process large collections of genome sequences efficiently.

Scientific Applications:

• Panallelome characterization: Characterizes total allelic diversity (panallelome) of bacterial species, including Salmonella enterica, Mycobacterium tuberculosis, Pseudomonas aeruginosa, and Staphylococcus aureus.
• Microbial genomics: Supports analyses of genetic variation relevant to disease mechanisms, antibiotic resistance, and vaccine development.

Methodology:

Performs exact-match proteomic compression, ranks protein sequences by observed exact matches in public genomes to compute a GNU score, classifies genomes based on these comparisons, and outputs whole-protein allele reports.