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Nucleic Acids Res. 2014 Jul;42(Web Server issue):W361-7. doi: 10.1093/nar/gku406. Epub 2014 May 14.

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

Author information

1
Department of Biology, Technion - Israel Institute of Technology, Technion City, Haifa 32000, Israel.
2
Department of Molecular, Cellular and Developmental Biology, UCSC, Santa Cruz, CA, USA.
3
Center for Biomolecular Science & Engineering, UCSC, Santa Cruz, CA, USA.
4
Department of Biology, Technion - Israel Institute of Technology, Technion City, Haifa 32000, Israel yaelmg@tx.technion.ac.il.

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.

PMID:
24829458
PMCID:
PMC4086114
DOI:
10.1093/nar/gku406
[Indexed for MEDLINE]
Free PMC Article

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