Predict Motif
Download Executable
Implementation Notes

Predict a Motif

This tool allows you to predict a structural motif common to a set of RNA sequences. The resulting motifs includes information on both RNA sequence and structure. Motifs are described both graphically and by a data file containing information on the underlying probabilistic model.

The motif prediction algorithm initally looks for structural elements which are common to the input RNAs, and then employs an EM algorithm to refine the resulting probabilistic model. Full details on the prediction algorithm are described in Rabani et. al, Computational prediction of RNA structural motifs involved in post transcriptional regulatory processes, Proc Natl Acad Sci U S A., September 2008. The tool is limited to uploading 5000bp sequences (25000bp is the maximum length of allowed uploaded structures, there are no restrictions on negative sequences). For heavy-duty motif prediction, please download the standalone executable and run it on your own machine.

Paste sequences (fasta format) Or upload: Paste input example

Upload negative sequence

Use Vienna to predict structures
Use CONTRAfold to predict structures
Upload structures to use

Advanced Parameters

Number of motifs to predict
Stem size flexibility
Loop size flexibility
Background distribution

For problems and questions, please e-mail Eran Segal