RBPmap: a web server for mapping binding sites of RNA-binding proteins

TLDR

RNA‑binding proteins regulate gene expression by binding specific sites on mRNAs and non‑coding RNAs, yet predicting these sites remains a major challenge. This study introduces RBPmap, a freely accessible web server for accurate prediction and mapping of RBP binding sites. RBPmap, built for human, mouse, and Drosophila genomes, lets users select or upload motifs, then applies a weighted‑rank algorithm that accounts for site clustering, conservation, and a position‑specific background model tailored to genomic regions. Benchmarking on high‑throughput RNA‑binding data demonstrates that RBPmap achieves high accuracy.

Abstract

Regulation of gene expression is executed in many cases by RNA-binding proteins (RBPs) that bind to mRNAs as well as to non-coding RNAs. RBPs recognize their RNA target via specific binding sites on the RNA. Predicting the binding sites of RBPs is known to be a major challenge. We present a new webserver, RBPmap, freely accessible through the website http://rbpmap.technion.ac.il/ for accurate prediction and mapping of RBP binding sites. RBPmap has been developed specifically for mapping RBPs in human, mouse and Drosophila melanogaster genomes, though it supports other organisms too. RBPmap enables the users to select motifs from a large database of experimentally defined motifs. In addition, users can provide any motif of interest, given as either a consensus or a PSSM. The algorithm for mapping the motifs is based on a Weighted-Rank approach, which considers the clustering propensity of the binding sites and the overall tendency of regulatory regions to be conserved. In addition, RBPmap incorporates a position-specific background model, designed uniquely for different genomic regions, such as splice sites, 5' and 3' UTRs, non-coding RNA and intergenic regions. RBPmap was tested on high-throughput RNA-binding experiments and was proved to be highly accurate.