how to predict hcv ires rna secondary structure from sequencing

Question

[ismaeilmohamed304]

hi

i have been extracted the rna from my blood samples collected from patients

and now i sequenced it and i have the sequence results (bidirectional direct sequencing )

my question is i want to predict the 2ry structure of these rna sequences (ires region )and know it there is any diffrences among different genotypes

thanx

[Michael]

Do you mean Iron Response Element by IREs region or Internal Ribosome Entry Site? Anyway, you should explain the acronyms used, especially for these short acronyms, not everyone can be expected to be accustomed with. Therefore, as a general recommendation to all users, please avoid acronyms or explain them in the text.

[ismaeilmohamed304]

hi thanx for ur appropriate response

i mean Internal Ribosome Entry Site in hcv and how or what software i can use to predict the 2ry structure

Answer 1

[Asaf]

It should be pretty simple. You can use the Vienna package for that, specifically RNAup which can give you the accessibility of each region in your sequence. I used RNAfold and analyzed the base-pairing matrix to get the same results (it was much faster). I have an implementation of it in my github https://github.com/asafpr/RNA/blob/master/structure.py

Taking the sequence of the IRES + 50 nt upstream and downstream should be enough, more distant RNA usually won't influence the structure.