Inverse folding of a single RNA

Designing RNA-RNA interaction switch

This design explores the sequence space to find RNA sequences that fold into the target structures in silico.
This design uses RactIP to predict secondary structures.
An external pseudoknot (eg an intermolecular pseudoknot including a kissing-hairpin) is allowed (whereas pseudoknots within each sequence is not allowed).
Examples of runtimes can be browsed here.
Current limit of this server is >= 20 nt and <= 230 nt. If you use this web server, please cite these papers.
Step 1: Input your targets to the following form in S+ notation :
(If you would like to directly specify the targets in the standard dot-bracket notation, you can skip Step 1 & 2 and go to Step3).

Line 1: The target joint structure of two RNAs
Line 2: Two target structures (for two single RNAs)
Using structure constraints of RactIP, intermolecular base pair formation is prohibited to predict the structure of the two single RNAs
Line 3 and more lines (optional) : structure and/or sequence motifs



 


Step 2: Click the above button to automatically generate your target(s) and sequence constraints in the standard dot-bracket notation; the generated structures and constraints are displayed in the form shown below.

Step 3: Confirm (or input) your targets in the following form (the targets are written in the standard dot-bracket notation [*?+ are also allowed]):
Line 1: The target joint secondary structure of two RNAs
Line 2: Two target secondary structures (for two single RNAs)
Line 3: Sequence constraints



The central value of desired G+C content (%):
  The half-range of the allowed G+C content (%):


GA population size:


Initial random number:


Prohibited sequence motifs (if multiple motifs are specified, please concatenate them with comma.):


Prohibited polynucleotide tracts. Those with the length (in nucleotides) longer than the value specified here are prohibited:  


PolyA tract is:  
  PolyC tract is:  
  PolyG tract is:  
    PolyU tract is:  



Step 4: Click the next button to submit your design!