RNA-Decoder is the first comparative method, which explicitly takes the known protein-coding context of an RNA-sequence alignment into account in order to predict evolutionarily conserved secondary-structure elements, which may span both coding and non-coding regions. On known secondary structures, RNA-Decoder shows a sensitivity similar to the programs Mfold, Pfold and RNAalifold. When scanning the entire genomes of HCV and polio virus for structure elements, RNA-Decoder's results indicate a markedly higher specificity than Mfold, Pfold and RNAalifold

Input Multiple Sequence Alignment (with optional annotation)

Paste a multiple sequence alignment of one or more sequences in FASTA format (up to 200kb total). An optional annotation can be provided, which should be a FASTA entry consisting of 1, 2, and 3 to indicate codon positions (or just 3 for non-coding regions). Click for example

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(Optional) Phylogenetic Tree

Paste a phylogeny tree in Newick format. All species must match those in both alignments. Click for example

One will be computed if no tree is given (and can be retrieved in the results tar-ball).
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Prediction Mode

Choose mode RNA-Decoder should run in:

Fold acts like a normal RNA secondary structure predictor, giving a single set of mutually compatible basepairs.
Scan will predict the probability of each positions being basepaired.
Note: For efficiency the input will be split into 600 bps side windows, created by sliding 200 bps each time for both modes.

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