Are there any RNA secondary structure prediction programs for long sequences?

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Jaswinder Singh

You can try LinearFold and LinearPartition predictors. Both are available free with web server at http://linearfold.org/ and standalone program at https://github.com/LinearFold. LinearFold and LinearPartition are quite fast for RNA secondary structure prediction as computational time is linearly scaled as a function of the length of a sequence.

Gerhard Steger

RNA structure prediction gets less reliable with increasing sequence length (>500 nt). This I would recommend to search for thermodynamically stable motifs in viral RNAs of kb lengths. This is, for example, possible with rnalfold or rnaplfold, which are part of the Vienna package (https://www.tbi.univie.ac.at/RNA/).