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I was rooting through the literature, but there is too much work on the topic of detecting loops in RNA and the RNA helices that go with them. Can anyone point to a good review on this topic or even better describe some better performing algorithms?

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What exactly do you mean by loops? Just unstructured parts of the RNA (= not in any base pairs)? – Mad Scientist Dec 3 '13 at 21:00
A loop in this case would be the result of an RNA helix from a single stranded RNA. The loop would be the result of the strand forming a helix by itself. – shigeta Dec 4 '13 at 6:03
So you only need to find the helices, from there identifying the loops is trivial. Can the loops have interactions with other parts of the RNA, e.g. pseudoknots? If not, any secondary structure prediction program like mfold should suit your purpose. – Mad Scientist Dec 4 '13 at 6:30
just looking for helices. i wasn't aware that was trivial.. is mfold accurate? – shigeta Dec 5 '13 at 6:08
As an improvement to what @WYSIWYG mentioned, PARS is fairly low resolution since it is still enzyme based. The newer in vivo SHAPE or DMS-seq methods are much better and more informative. – bobthejoe Dec 11 '13 at 2:56

I frankly don't trust Mfold or RNAfold for finding structure. There are just too many false positives and without experimental verification, it's not reliable. For finding hypothetical local structure, it's great. However to find evolutionary conserved structure MSA methods like what has been used with Rfam are a more suitable way.

Since you asked for Reviews, any of Sean Eddy's Rfam updates are good. I also suggest checking out

But for now, I think Revolutions in RNA Secondary Structure Prediction by David Mathews who developed the Turner rules and Mfold is a good start.

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thanks - this sounds like details are important – shigeta Dec 11 '13 at 0:42

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