This is a test version of Biostars. For the public version, visit https://www.biostars.org.
How ViennaRNA Package deal with character other than AUGC in RNA secondary structure prediction?

I have a RNA sequence as following, where "o" connects two RNA sequences.

UAGGGoooooooAGUU

Most of the RNA secondary structure prediction tools do not allow characters other than AUGC, but I find out the ViennaRNA allows "o" and can predict structure with it. But I am wondering how ViennaRNA (RNA2Dfold) deal with "o". I can not find any clues on ViennaRNA website. Please help me if you know the answer:) Thanks in advance.

rna-seq sequence
• 2,656 views • link
updated by Ram Ram • written by wyj.jackson • wyj.jackson

1 answer

non AUGC bases are considered part of the RNA molecule, but they cannot form any pair. they can be in a loop separating two matching stretches, like in the following example:

AAAAAAAAAAooooooooTTTTTTTTTT
((((((((((........))))))))))

which is not the same as if they were completely ignored:

AAAAAAAAAATTTTTTTTTT
((((((((....))))))))

can I ask you what do these o represent in your sequence?

• 0 views • link
updated by Ram Ram • written by Martombo Martombo

Thanks for your reply.

Do you know how those non AUGC bases influence the energy model of hairpin, interior and multi loops in the package? Also treat them as unpaired bases?

For "o"s, our collaborator said that they are physically very flexible and can link two RNA sequences.

• 0 views • link
updated by Ram Ram • written by wyj.jackson • wyj.jackson

according to how your collaborators described it, it looks like the ViennaRNA package deals with them as you want it to. They are in all respects like unpaired bases.

• 0 views • link
written by Martombo Martombo

Log in to answer this question.

More posts like this