I'm looking for software that will find the single most stable stem-loop in an RNA sequence. I have tried the (M)FOLD programs of Dr. M. Zuker, but they don't
really do this. The structures consist of many weak hairpins, the sum of which
yields a modest negative free energy for my sequences. I've also tried a
program called stem-loop and fed the individual hairpins to FOLD. This proved
too time consuming (hundreds of stem-loops are found) and the structures are
weak. I'd prefer to systematically search for all single hairpins in the range of say, -15 to -20 kcal/mol free energy-about 30% less stable than the aggregate structures.
Thanks in advance for any help. Mark A. Hess
mhess at hsc.usc.edu