Department of Biology, Technion - Israel Institute of Technology, Technion City, Haifa 32000, Israel.
Department of Molecular, Cellular and Developmental Biology, UCSC, Santa Cruz, CA, USA.
Nucleic Acids Res. 2014 Jul;42(Web Server issue):W361-7. doi: 10.1093/nar/gku406. Epub 2014 May 14.
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.
基因表达的调控在许多情况下是通过 RNA 结合蛋白（RBPs）执行的，这些蛋白既可以与 mRNA 结合，也可以与非编码 RNA 结合。RBPs 通过 RNA 上的特定结合位点识别其 RNA 靶标。已知预测 RBPs 的结合位点是一个主要挑战。我们提供了一个新的网络服务器 RBPmap，可通过网站 http://rbpmap.technion.ac.il/ 免费访问，用于准确预测和绘制 RBPs 的结合位点。RBPmap 是专门为在人类、小鼠和黑腹果蝇基因组中绘制 RBPs 而开发的，尽管它也支持其他生物体。RBPmap 允许用户从大量实验定义的基序数据库中选择基序。此外，用户还可以提供任何感兴趣的基序，无论是共识序列还是 PSSM。基序映射的算法基于加权排序方法，该方法考虑了结合位点的聚类倾向和调节区域的整体保守倾向。此外，RBPmap 还包含一个位置特异性背景模型，该模型专为不同的基因组区域（如剪接位点、5' 和 3'UTR、非编码 RNA 和基因间区域）设计。RBPmap 已在高通量 RNA 结合实验中进行了测试，证明其具有高度准确性。
