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(n7) and space O(n4), by employing the Fast Fourier Transform (FFT),FFTbor2D computes the same value in time O(n5) and space O(n3).

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"
E. Senter, I. Dotu, P. Clote
submitted to J Math Biol.
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