Alignment Based Secondary Structure Prediction
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.
2 answers
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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Alex Paciorkowski
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