RNA–RNA interactions considering Seeds and Accessibility

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PredictionIntaRNA EvaluationIntaRNAeval Mutation DesignCopomuS

Predict interactions for all query–target sequence pairs.

Query RNA5′ to 3′

or drop in the field

Start index No sequence entered

Target RNA5′ to 3′

or drop in the field

Start index No sequence entered

Plain sequence or multi-FASTA (prediction only), A/C/G/U/T/N. Up to 50 records per field and 2–5,000 nt per record; longest selected query × longest selected target ≤ 1,000,000. FASTA names stop at the first whitespace. Seed predictions also require at least as many nucleotides as seed base pairs. Signed start indices apply to every record on that strand; negative indexing skips zero.

Input Parameters:

Results

Enter your sequences or choose an example, then compute.

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Computation diagnostics

RNA–RNA interactions considering Seeds and Accessibility

Compensatory mutation settings

Results

Interaction visualization

Compensatory-mutation visualization

Additional output files

Computing interactions