bioinformatics tools to connect modifications on RNA to its structure

Question

[suneetamodekurty77]

Hi

I have modifications on RNAs and also have their predicted structures. Is there any tool that can map the modifications to structure (to see whether the modifications fall on the paired or the unpaired regions)?

Thank you

[shawn.w.foley]

What format do you have the data in? I'm not familiar with any software to do the analyses for you, but if you have the modifications and structure data in a BED format an intersectBed will show you the overlap. What's the end goal, identifying which modifications correspond to paired/unpaired nucleotides or something further?

Answer 1

[suneetamodekurty77]

my modifications data is in the bed format. yes, that's the end goal, to identify which modifications correspond to paired and which correspond to unpaired nucleotides. So, I want to know how I can do that. Is there a software?My structures data is in the form of .ct files.

https://rna.urmc.rochester.edu/Text/TurboFold.html

Any suggestions or help will be highly appreciated. Thank you!

[shawn.w.foley]

I'm not familiar with a .ct file, could you post a few lines from it?

Answer 2

[suneetamodekurty77]

I have modifications as bedfiles and have structure as .dot bracket format Dot bracket format is as below ...((((......)))).... Somewhat like the above each dot and each bracket corresponds to either A,C,G or T So also a .ct file has a number that corresponds to to the bases. So I have modifications in bed file and structure as dot bracket notations. I am looking at how I can map the modifications to structure to see if the modifications are on the paired or the unpaired regions of my RNA. How can I do it in python? Any suggestions are welcome. Thank you!