Welcome to the RNA parametric structure webserver!

Given an RNA sequence, RNAhairpin computes, simultaneously for each integer 0 ≤ k ≤ Kmax, the minimum free energy structure MFE(k) and the partition function Z(k) over all secondary structures having exactly k hairpins. Similarly, RNAmloop computes, simultaneously for each integer 0 ≤ k ≤ Kmax [0 ≤ d ≤ Kmax] the minimum free energy structure MFE(k) [resp. MFE(d)] and partition function Z(k) [resp. Z(d)] over all secondary structures having exactly k multiloops [resp. maximum order d multiloops]. Additionally, the web server computes samples from the Boltzmann ensemble.

The corresponding Boltzmann probabilities of hairpin and multiloop formation can be used as additional features in noncoding RNA gene finder.