Looking for IRES in UTRs

[ucpete]

I'm not sure if this is the right forum in which to be posting this question but I'm sure there are some RNA folding gurus out there. I've got some viral UTRs and I'm looking to see if there are any canonical IRES in them. I'm doing so by playing with some RNA folding software (mFold, NUPACK, pknotsRG, and others), but the folds I get are sort of wild and don't resemble IRES. I can't decide if that's because there are no IRES or if I'm not tweaking parameters correctly! Has anyone done this successfully? Does anyone have any advice for this RNA folding noob?

Thanks,

ucpete

[ucpete]

I should add that one of the UTRs I'm particularly interested in has no detectable sequence homology to any other known UTR sequences, so the "fold by homologous inference" strategy is out the window. I've also considered folding small pieces of it one at a time and sort of combining the folded sub-pieces afterwards as some of the weirdness in the folds I have generated thus far are long range interactions between regions far apart in primary sequence (that I wouldn't expect to see in a well-behaved IRES-containing UTR).