Welcome to the RNAxs Webserver! This server will help you to design potent siRNAs to knock down your gene(s) of interest. RNAxs is based on the RNAplfold program to assess the mRNA target site accessibility.

RNAxs was trained on two different datasets, one targeting 3'UTRs and the other one designed to repress coding sequences only.

Simply paste your sequence in FASTA format(!) below. Reasonable default values for siRNA design criteria are pre-chosen, which have shown to give an optimal separation of functional and non-functional siRNAs. To obain more information about the meaning of the design options hover your mouse over the help

You can test the server using this sample sequence.

Sequence Input

Paste your sequences here (at most 20000 nts):Clear!


Design Options
8nt (Seed) Accessibility Threshold help
16nt Accessibility Threshold help
Self Folding Energy help
Sequence Asymmetry help
Energy Asymmetry help
Free End help
Custom Sequence Rules help

Output Option
Maximal Number of siRNAs help
E-Mail address (optional): help

We appreciate your feedback. Please send comments to:
Hakim Tafer | htafer@tbi.univie.ac.at | TBI
Gregor Obernosterer | gregor.obernosterer@imba.oeaw.ac.at | IMBA
Stefan L Ameres | stefan.ameres@univie.ac.at | MFPL