RBPmap

RBPmap predicts and maps RNA-binding protein (RBP) binding sites across genomic contexts to analyze RBP–RNA interactions in mRNAs and non-coding RNAs.

Key Features:

• Organism Support: Optimized for human, mouse, and Drosophila melanogaster genomes, with extended functionality for other organisms.
• Motif Selection: Supports a database of experimentally validated motifs and accepts custom motifs in consensus format or as Position-Specific Scoring Matrices (PSSMs).
• Advanced Algorithm: Employs a Weighted-Rank approach that evaluates the clustering propensity of binding sites and accounts for conservation tendencies of regulatory regions.
• Position-Specific Background Model: Integrates a background model tailored to genomic regions including splice sites, 5' and 3' untranslated regions (UTRs), non-coding RNAs, and intergenic areas.

Scientific Applications:

• RBP Binding Site Mapping: Predicts and maps RBP binding sites with validation against high-throughput RNA-binding experiments.
• Post-transcriptional Regulation Studies: Supports analyses of how RBPs influence gene expression at the post-transcriptional level.
• Non-coding RNA Function: Enables investigation of RBP interactions with non-coding RNAs to assess their functional roles.

Methodology:

Applies a Weighted-Rank algorithm that evaluates clustering propensity and conservation patterns and combines these scores with a position-specific background model tailored to splice sites, 5' and 3' UTRs, non-coding RNAs, and intergenic regions.