RBPmotif web server

RBPmotif server runs in two modes:
  • De novo motif finding with RNAcontext algorithm to discover the sequence and structure preferences of the RBP of interest. [Left]
  • Secondary structure analysis to investigate whether a previously identified sequence motif is enriched in a particular structure context in bound sequences compared to unbound sequences. [Right]
Please make sure your input sequences conforms to the following limitations:
  • The minimum number of sequences in bound or unbound set is 50.
  • The maximum number of allowed sequences is 1000 (i.e. 1000 for bound and 1000 for unbound set).
  • The length of a sequence cannot be less than the motif length.
  • The maximum length of a sequence is 1500 nts.
  • Please see the help page for more information.

    Email (optional):


    If an email is given, we will email a notification when RNAcontext is finished running. Otherwise, a link will be given upon submission where the results will be posted.



    Please input sequences that are bound and not bound by the RBP of interest.


    Please include at least 50 sequences. RNAcontext may not run properly if there are not enough sequences provided.


    1) Paste a set of sequences (in FASTA format) that are bound by the RBP:



    Or upload a file in FASTA format





    2) Paste a set of sequences (in FASTA format) that are not bound by the RBP:


    Or upload a file in FASTA format



    3) Parameters for secondary structure prediction
    a) Structure Alphabet :
    b)   global local
           window >= span
    Choose one of the two options:



    This page is compatible with Google Chrome, Mozilla Firefox and Safari.
    If you find this web server useful please cite:
    Kazan H, Ray D, Chan ET, Hughes TR, Morris Q (2010) RNAcontext: A New Method for Learning the Sequence and Structure Binding Preferences of RNA-Binding Proteins. PLoS Comput Biol 6(7): e1000832. doi:10.1371/journal.pcbi.1000832