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
Thanks,
ucpete
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