RNA secondary structure prediction

Question

[kaur.devbio]

Hello,

Can anyone tell a tool which could predict the secondary structure of RNA which also take pseudouridine pairing with adenine or any nucleotide (A~ѱ, N-ѱ) in account.

Answer 1

[Charles Warden]

I don't know, but I would probably start by contacting the developers for the most popular RNA secondary structure prediction tools. If this is a common request, maybe it is taken into consideration in the latest version of their program.

If it helps, I believe these are the most commonly used tools:

• http://mfold.rna.albany.edu/?q=mfold
• http://www.tbi.univie.ac.at/RNA/RNAfold.html

Alternatively, you can check if the same group has developed a different program that might address this issue (for example, I believe the developers of Mfold actually consider UNAfold to be a better option, but I don't recall why).

[kaur.devbio]

Thanks for writing Charles Warden,

I already mailed to the developers of RNAfold as well as Mfold regarding the same issue bust still waiting for their response.