Question: RNA strucuture prediction
1
gravatar for bandanaschapagain
2.4 years ago by
bandanaschapagain30 wrote:

Hil All, I am trying to predict the RNA structure using the DNA sequence. For that I used Vienna and RNA web server prediction. But the RNA structure is not predicted properly. The end goal of my analysis is to identify which region of DNA sequence fall into stem loop strutcure. Is there any other way I could try?

I appreciate your help. Regads, Bandana

rna-seq • 725 views
ADD COMMENTlink written 2.4 years ago by bandanaschapagain30

Are you transcribing the sequence yourself first? There are loads of RNA structure predictors, but I've never seen a really thorough comparison between all of them, and a lot of the predictions are anyone's guess really.

How do you know the structure isn't predicted properly if you don't know where the stem-loops are?

Some popular ones in my lab however, include gardenia, not least because it has one of the nicer visual outputs, and CONTRAfold

ADD REPLYlink written 2.4 years ago by Joe16k

I am just using the DNA sequence and not transcribing it. For my case its wrong because I am looking a tool to say me about the nucleotides position where the stem-loop structure appears but Vienna it just gives me "some structure" but nothing about the base position. I am really trying hard to find one tool which gives me the presentable RNA Structure.

ADD REPLYlink written 2.4 years ago by bandanaschapagain30

Is this for microRNA prediction or something else? The tools can vary based on your target RNA type. If the structure is completely unknown it is difficult to be certain of the final structure, hence it is a "prediction". I would suggest that you try out multiple structural prediction tools on a very well annotated RNA sequence (or its original DNA sequence), see which one performs the best and use that to do your predictions.

ADD REPLYlink modified 2.4 years ago • written 2.4 years ago by diveena0

It's just for the RNA structure prediction. I am trying hard to find one tool which allows me to know the base position for stem-loop structures of the RNA.

ADD REPLYlink written 2.4 years ago by bandanaschapagain30

Dot-bracket notation, such as that output by Gardenia is on a per-base basis. You could easily write a little script to enumerate this if you wanted to get the positions present within loops and stems etc.

ADD REPLYlink written 2.4 years ago by Joe16k
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