CompariPSSM

CompariPSSM quantifies the similarity between motif-binding determinants using sliding window PSSM-PSSM comparison and a probabilistic framework for motif analysis tasks.

Key Features:

• PSSM-PSSM Comparison: Quantifies similarity between motif-binding determinants using sliding window PSSM-PSSM comparison.
• Probabilistic Scoring: Scores PSSM similarity using a randomisation-based probabilistic framework.
• Peptide Classification: Validates motif classes through peptide classification.
• Peptide Clustering: Groups functionally related conserved disordered regions through peptide clustering.
• Benchmarking: Benchmarks experimental motif discovery methods.

Scientific Applications:

• Motif Annotation: Supports annotation of short linear motifs (SLiMs) through motif-binding determinant comparison.
• Motif Classification: Classifies motifs by comparing motif-binding determinants.
• Motif Clustering: Clusters motifs based on quantitative PSSM similarity rather than consensus similarity alone.
• Motif Discovery: Aids discovery of short linear motifs that mediate low-affinity protein-protein interactions.
• Benchmarking Experimental Methods: Evaluates and benchmarks experimental motif discovery methods using curated and proteomic data.
• Peptide Classification: Validates motif classes by classifying peptides.
• Peptide Clustering: Groups functionally related conserved disordered regions.

Methodology:

CompariPSSM uses sliding window PSSM-PSSM comparison and scores PSSM similarity using a randomisation-based probabilistic framework. The tool was benchmarked on curated data from the eukaryotic linear motif database and experimental data from proteomic peptidephage display.