Interesting Question about RNAhybrid

Question

[biolab]

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!

[Devon Ryan]

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).

[biolab]

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.

[baurumon]

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

[ATpoint]

Please open a new question, adding the necessary details after browsing the web for help towards text file manipulation with eg. awk.

Answer 1

[tomluec]

It seems that the authors of RNAhybrid have extended the original MFE equation. You can see a publication on the matter here.