Bipartite Motif Finder

Bipartite Motif Finder identifies multivalent sequence motifs and their spatial dependencies in RNA and DNA sequences to characterize cooperative binding by RNA-binding proteins.

Key Features:

• Multivalent Binding Analysis: Focuses on RNA-binding proteins (RBPs) that use multivalent or cooperative binding strategies to increase specificity and affinity.
• Thermodynamic Modeling: Employs a thermodynamic model tailored for RBPs with two cooperatively interacting RNA-binding domains.
• Spatial Geometry Learning: Infers the spatial geometry between binding sites from bound RNA sequences.
• Consistency with Known Motifs: Identifies bipartite motifs that align with previously reported motifs and known binding behaviors.

Scientific Applications:

• RBP specificity characterization: Dissects how bivalent binding by RBPs contributes to sequence specificity and binding affinity.
• Regulatory mechanism investigation: Supports studies of gene regulation, post-transcriptional modifications, and other cellular processes mediated by protein–RNA interactions.

Methodology:

Uses a thermodynamic framework modeling cooperative binding of RBPs with two RNA-binding domains and analyzes bound RNA sequences to learn spatial configurations of bipartite motifs.