FFTbor2D swMATH ID: 11717 Software Authors: E. Senter, I. Dotu, P. Clote Description: 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). Homepage: http://bioinformatics.bc.edu/clotelab/FFTbor2D/index.spy Related Software: NNDB; ViennaRNA; MODENA; FFTbor; MSMBuilder; ERD; KFOLD; RNAexpNumNbors; Rfam; KineFold; RNA2Dfold; FFTW; LAPACK Cited in: 2 Publications Cited by 4 Authors 2 Clote, Peter G. 1 Bayegan, Amir H. 1 Dotú, Iván 1 Senter, Evan Cited in 1 Serial 2 Journal of Mathematical Biology all top 5 Cited in 6 Fields 2 Probability theory and stochastic processes (60-XX) 2 Computer science (68-XX) 2 Biology and other natural sciences (92-XX) 1 Numerical analysis (65-XX) 1 Mechanics of deformable solids (74-XX) 1 Quantum theory (81-XX) Citations by Year