GibbsCluster

GibbsCluster performs simultaneous alignment and clustering of peptide sequences to discover conserved sequence motifs and resolve multiple specificities in peptidome datasets for analysis of receptor–ligand interactions.

Key Features:

• Simultaneous clustering and alignment: Clusters peptide sequences and aligns them to reveal conserved sequence motifs.
• Handling of insertions and deletions: Incorporates insertions and deletions to account for motif length variation within input peptides.
• Optimal cluster identification: Returns the optimal number of clusters together with sequence alignments and characterizing motifs.
• Customizable analysis parameters: Provides adjustable penalties for small clusters and overlapping groups and an option for a trash cluster to filter outliers.
• Deconvolution of peptidome specificities: Deconvolutes multiple specificities in large-scale peptidome data, including datasets generated by mass spectrometry.

Scientific Applications:

• Receptor–ligand interaction analysis: Identifies and characterizes sequence motifs relevant to receptor–ligand binding and signaling pathways.
• Peptidomics and mass spectrometry: Resolves multiple binding specificities and motifs within peptidome datasets derived from mass spectrometry.
• Molecular basis of biological processes and diseases: Reveals peptide-binding specificities that inform the molecular basis of biological processes and disease mechanisms.

Methodology:

Unsupervised motif discovery using statistical clustering of peptide sequence similarities with explicit modeling of insertions and deletions.