## Welcome to the FFTbor2D webserver!

Given an RNA sequence having metastable secondary structures A,B, the
program FFTbor2D computes the ensemble free energy E(x,y)=-RT log Z(x,y),
taken over all secondary structures having base pair distance x from A,and base pair distance y from B.
While the Vienna RNA Package
program RNA2Dfold computes the ensemble free energy in time O(n^{7}) and
space O(n^{4}), by employing the Fast Fourier Transform (FFT),FFTbor2D computes the same value in time O(n^{5}) and
space O(n^{3}).

Note: If the user needs the structures MFE(x,y), having minimum free energy over all structures at distance x from A and y from B, then RNA2Dfold should be used instead of FFTbor2D.

Tarball for source code is here: fftbor_tagged_v2.0.tar.

If you use FFTbor2D in your work, please cite:

"RNA folding pathways and kinetics using 2D energy landscapes"Full web server is under construction!

E. Senter, I. Dotu, P. Clote

submitted toJ Math Biol.