Forum:Secondary Structure Prediction software RNA/DNA

Question

[14134125465346445]

This is a list of software packages and utilities to predict the secondary structure of RNA/DNA molecules:

• http://rna.tbi.univie.ac.at/
• http://rna.urmc.rochester.edu/RNAstructure.html
• http://mfold.rna.albany.edu/

Answer 1

[Manvendra Singh]

I have a concern that which one would be more suitable or reliable to use if I have 300-700 bp long RNA sequence which is not classified yet ?

Once we get secondary structures of RNA then I would also be curious to know that which proteins could probably bind to the found secondary structures.

If we get more structures and we find different sets of proteins binding (in silico), then which one could be trusted ?

I am little lost, but would be great to have answers/discussions.

[sumithra.das]

I have same concern now, trying for reliable insilico tools for Secondary structure prediction of mRNA sequences ? Once if i get, how to know which RBP's binds the modelled structures ? then how to confirm( insilico) the bound RBP's to mRNA's could be trusted?

Thanks