rna Map Analysis
and Plotting Server

rMAPS is a web server that systematically generates RNA-maps for the analysis of RNA-binding proteins (RBPs) binding sites which have position-dependent functions. Users can easily perform analysis of binding sites around differential alternative splicing events for over 100 of known RBPs. rMAPS can also analyze CLIP-seq peaks around differential alternative splicing events to generate an RNA-map of CLIP-seq experiment.


[ Overall pipeline of rMAPS2 ]


rMAPS is a computational motif enrichment analysis tool for RNA-binding proteins using RNA-seq and CLIP-seq data.

rMAPS in Action


Jae Y. Hwang, Sungbo Jung, Tae L. Kook, Eric C. Rouchka, Jinwoong Bok, Juw Won Park, rMAPS2: an update of the RNA map analysis and plotting server for alternative splicing regulation, Nucleic Acids Research, 2020, , doi: 10.1093/nar/gkaa237

Juw Won Park, Sungbo Jung, Eric C. Rouchka, Yu-Ting Tseng, Yi Xing, rMAPS: RNA Map Analysis and Plotting Server for Alternative Exon Regulation. , Nucleic Acids Research 2016 doi: 10.1093/nar/gkw410


  3/20/2020 Release of rMAPS v2.2.0
  • Employed an option of plot type, which separates Motif Score & p-Val in Motif Map and Peak height & p-Val in Clip Map.
  12/5/2019 Release of rMAPS v2.1.2
  • Added an assemblies of pig (susScr11) and cow (bosTau9) to Motif Map.
  9/14/2019 Release of rMAPS v2.1.0
  • Fixed a bug related to no motif count error. It now generates a map even when motif counts are zero throughout the region.
  8/29/2019 Release of rMAPS v2.0.0
  • Support all 5 major types of alternative splicing events (SE, MXE, A5SS, A3SS, and RI).
  • Employed multi-threading for significant reduction in running time (takes less than 4 minutes for all 5 AS types together).
  2/24/2018 Release of rMAPS v1.2.7
  • Added more assemblies of chicken (galGal5 and galGal6) to Motif Map.
  12/7/2017 Release of rMAPS v1.2.5
  • Added more assemblies of Frog (xenLae2 and xenTro9) and Rice plant (oSa7) in Motif Map.
  11/22/2017 Release of rMAPS v1.2.2
  • Added more assemblies of Zebrafish (danRer11) and Arabidopsis Thaliana plant (araTha1) in Motif Map.
  7/14/2017 Release of rMAPS v1.2.0
  • Fixed a bug related to handling “User Input” option in Moif Map.
  3/28/2017 Release of rMAPS v1.1.0
  • MotifMap plots are sorted by minimum p-value (up vs bg) of each RBP on the target exon region. RBP with the smallest p-value on the target exon appears first.
  • To facilitate candidate RBP search process, MotifMap now provides text files listing RBPs with their smallest p-values in three regions of interest. (i.e., upstream intron, target exon, and downstream intron.)
  • Users can sort text files by a column (region) to find RBPs significantly enriched in that region.
  5/12/2016 Release of rMAPS v1.0.0
  • First official version of rMAPS is released.



QUICK RUN with Testdata



Contact: Professor Juw Won Park ( juw {dot} park {at} louisville {dot} edu )