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

By Inbal Paz, I. Kosti, M. Ares, Melissa S. Cline, Y. Mandel-Gutfreund. Nucleic Acids Res., 2014

532 citations recorded by the source corpus.

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.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/fd73753ed42464b61fdc829b96c8b6c5ef4bcd37

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Molecular Biology

  1. Manuela Helmer-Citterich
  2. Alessio Colantoni
  3. Fabrizio Ferrè

Citations in the corpus