Interesting Question about RNAhybrid
Hi everyone,
I am implementing RNAhybrid with the following miRNA and target sequences.
>target
ACGGGGGUUUATCGUAUC
>mir
GAUACGAUAACCCCGU
The output is as follow.
target 5' GUU 3'
ACGGGG UAUCGUAUC
UGCCCC AUAGCAUAG
miRNA 3' A 5'
I think the result is obviously wrong because the following structure is more stable.
target 5' GU 3'
ACGGGG UUAUCGUAUC
UGCCCC AAUAGCAUAG
miRNA 3' 5'
Where is the problem? Could export give some suggestions or ideas? THANKS!
1 answer
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I'm not so sure the first result is obviously wrong. It's questionable whether the constrained bond angles would permit the second structure (perhaps they would, I don't pretend to be an expert in RNA secondary structure).
Hi, Devon, thanks for comments. Yes, now i agree that the first structure is not wrong. I checked MFE of these two structures, and they have the same MFE. So both are similarly stable. I am just wondering why the top hit is the first structure.
Hi, I have used RNAhybride to predict miRna to target desired sequence. Can anyone help me in the way to parse output by column as below.
target: NC_031978.2:30702661-30704116 | miRNA : oni-miR-10613 | mfe: -26.5 kcal/mol | p-value: 0.095468
Please open a new question, adding the necessary details after browsing the web for help towards text file manipulation with eg.
awk.