RNAex specifications


Unique identifier OMICS_11686
Name RNAex
Alternative name RNA secondary structure prediction enhanced by high-throughput experimental data
Interface Web user interface
Restrictions to use None
Input data To use RNAex, users are required to first select two matched probing datasets and a folding method. Then, users need to input their transcripts of interest for structure prediction, by providing the transcript IDs or the genomic locations in GTF format. RNAex can run multiple transcripts in parallel. RNAex accepts the following transcript IDs for known transcripts: TAIR (v10) ID for Arabidopsis transcripts, SGD (SacCer2) ID for yeast transcripts, GENCODE (v19 for DMS-seq and v12 for PARS data) ID for human transcripts and GENCODE (v2) ID for mouse transcripts. RNAex also accepts genomic locations in GTF format for novel transcripts.
Computer skills Basic
Stability Stable
Maintained Yes


  • Plants and Fungi
    • Arabidopsis thaliana
    • Saccharomyces cerevisiae
  • Primates
    • Homo sapiens
  • Rodents
    • Mus musculus



  • person_outline Rex Team <>

Publication for RNA secondary structure prediction enhanced by high-throughput experimental data

RNAex institution(s)
MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Center for Plant Biology and Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
RNAex funding source(s)
National Key Basic Research Program of China [2012CB316503]; National High-Tech Research and Development Program of China [2014AA021103]; National Natural Science Foundation of China [31271402, 31522030]; Tsinghua University Initiative Scientific Research Program [2014z21045]; Computing Platform of National Protein Facilities (Tsinghua University)

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