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Transat—A Method for Detecting the Conserved Helices of Functional RNA Structures, Including Transient, Pseudo-Knotted and Alternative Structures

Figure 11

Known RNA secondary structure and Transat predictions for the Cripavirus internal ribosomal entry site (IRES), RF00458, for a p-value threshold of .

Transat predicts the helices of the pseudo-knotted known structure correctly and also predicts several transient helices which suggest a co-transcriptional folding pathway (see numbering of helices above). All predicted transient helices (helices 4, 6 and 10) are mutually incompatible with a helix of the known RNA structure. Helix 4 may yield to helix 8, helix 6 to helix 7 and helix 10 to helix 12. The transient helices may thereby guide the formation of the known functional RNA structure.

Figure 11