Alignment Based Secondary Structure Prediction
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11.1 years ago
Cacau ▴ 520

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.

rna structure • 2.3k views
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11.1 years ago

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.

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7.0 years ago
ricovox ▴ 20

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).

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