PhyRepID

PhyRepID quantifies protein repeat evolution across orthologous proteins using comparative phylogenomics to characterize repeat expansions, contractions, and duplications.

Key Features:

• Detection of Protein Repeats: Detects a wide array of protein repeats, including repeats composed of Pfam structural domains and motifs.
• Enhanced Sensitivity and Precision: Optimizes sensitivity and precision of repeat unit detection specifically for groups of orthologous proteins (OGs).
• Phylogenetic Analysis Integration: Employs phylogenetic analysis and leverages phylogenetic signals to derive the protein repeat duplication (PRD) score.
• Quantitative Evolutionary Insights: Uses the PRD score to rank proteins by evolutionary dynamics, distinguishing rapidly evolving repeats such as zinc finger repeats from more conserved cooperatively-folding domain repeats like beta-propellers.
• Discovery of Novel Candidates: Confirms previously observed patterns in proteins such as KNL1 and PRDM9 and identifies novel rapidly evolving candidates including AHNAK, PRX, and SPATA31.

Scientific Applications:

• Comparative phylogenomic analysis: Quantifies repeat evolution across orthologous proteins from multiple vertebrate species (4939 OGs analyzed from 14 species) to study repeat expansions and contractions.
• Candidate prioritization for functional and evolutionary studies: Ranks proteins by repeat evolutionary dynamics to identify targets for follow-up functional and evolutionary investigation (e.g., KNL1, PRDM9, AHNAK, PRX, SPATA31).

Methodology:

Combines Pfam domain and motif detection with phylogenetic analysis and computes a protein repeat duplication (PRD) score from phylogenetic signals.