Batch verify hairpin structure
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20 months ago
153348734 • 0

I downloaded hairpin and mature sequence from miRBase and predicted the possible locations of some miRNAs in my genome. Now I want to verify the hairpin structure to filter these locations. RNAfold can give the results, but it can only verify them one by one. I want to ask if there is any software that can batch filter these locations? Thank you! enter image description here

miRNA • 590 views
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What do you mean by "verify" and by that the RNAfold can only verify then "one by one". The RNAfold will happily predict thousands of structures for thousands of your input sequences at once.

What is acceptable for you as "hairpins" is entirely different problem though. I'm not aware of any software that would classify structures as "hairpin" or "other", although, there is set of tools called RNAshapes and one of the functions (I think RapidShapes) is to extract abstract shapes (for example ((())) would be [] if I remember correctly.

Depending on what is acceptable for you as hairpin, you might be better of using custom script, that e.g. checks whether there is any ( character occurring after the first ) character in the dot bracket notation string (or vice versa). Beware, that this may hold true for mostly unpaired structures (even with only one or two basepairs), which is presumably not what you want, so setting some minimum number of base-pairs may be in order.

Hope this helps

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Thank you! I'm a novice and don't know much about miRNA.