Question: how to predict hcv ires rna secondary structure from sequencing
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gravatar for ismaeilmohamed304
3.2 years ago by
ismaeilmohamed30410 wrote:

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

rna-seq alignment sequence • 874 views
ADD COMMENTlink modified 3.2 years ago by Asaf6.5k • written 3.2 years ago by ismaeilmohamed30410
1

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.

ADD REPLYlink modified 3.2 years ago • written 3.2 years ago by Michael Dondrup47k

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

ADD REPLYlink written 3.2 years ago by ismaeilmohamed30410
0
gravatar for Asaf
3.2 years ago by
Asaf6.5k
Israel
Asaf6.5k wrote:

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.

ADD COMMENTlink written 3.2 years ago by Asaf6.5k
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