the Theoretical Biochemistry Group of the Institute for Theoretical
Chemistry at the Universty of Vienna has devised a public domain
program package, "The Vienna RNA Package", that can fold sequences
of almost arbitrary length PROVIDED you computer has enough
memory. The package not only calculates the minimum free energy
structure but it also computes the partition function and the
complete matrix of base pairing probabilities.
The programs run on a number of UNIX platforms as well a few
mainframes (such as IBM 3090 -- with a few trivial modifications
as some default header files have different names on these maschines).
It actually should work wherever you have gcc or another decent
ANSI C compiler.
We have been successfully folding 23S RNAs on an IBM RISC 6000/550
with 64MByte memory and the complete genome of the phage Qbeta on
an maschine with 256MByte.
The "Vienna RNA Package" is available as source code by anonymous
Peter F Stadler
Theoretical Biochemistry, Inst f Theoret. Chemistry, Univ Vienna, Austria &
The Santa Fe Institute, Santa Fe, NM, U.S.A.