Alignment Based Secondary Structure Prediction

Question

[Cacau]

I want to make a prediction of the 2nd struc of my RNA sequence. Does anybody know what software could be used to do it based on MSA? Thanks!

PS: Some 2nd structures of sequences in my MSA have been known. And I want to know 2nd structures of other sequences in the alignment.

Answer 1

[Alex Paciorkowski]

You can try some of the suggestions here: Tools To Model Rna Structure?

You can also look at RNAstructure, and see if it meets your needs.

Answer 2

[ricovox]

Look at the TurboFold, multilign and Dynalign tools in the RNAstructure package. I'm not sure which of those best fit your needs, but they all produce structures based on MSA (I think).