RBPmotif

RBPmotif identifies sequence and structure preferences of RNA-binding proteins (RBPs) from sets of bound and unbound RNA sequences.

Key Features:

• De novo motif finding: Learns discriminative sequence and structural binding motifs from bound versus unbound sequences using the RNAcontext algorithm and outputs inferred binding preferences and the predictive value added by structural information.
• Structure preference analysis: Evaluates whether instances of a known sequence motif are enriched in specific RNA structural contexts within bound sequences compared to unbound sequences.
• Statistical significance assessment: Compares structural contexts between bound and unbound sequences and reports the statistical significance of detected preferences.

Scientific Applications:

• RBP binding specificity elucidation: Dissects how RBPs recognize target RNAs by integrating sequence and RNA structural context.
• Post-transcriptional regulation studies: Links motif and structure preferences to gene regulation and post-transcriptional control mechanisms.
• Disease and therapeutic target investigation: Identifies altered RBP binding preferences that may inform disease mechanisms or potential therapeutic targets.

Methodology:

Performs de novo motif discovery using the RNAcontext algorithm on bound versus unbound sequences and performs structure preference analysis of known motifs by comparing structural contexts between bound and unbound sequences with statistical significance testing.