Transat—A Method for Detecting the Conserved Helices of Functional RNA Structures, Including Transient, Pseudo-Knotted and Alternative Structures
Known RNA secondary structure and Transat predictions for two hairpin-like known structures, the small nucleolar RNA snR76 for a p-value threshold of (left, RF01209) and the bacterial signal recognition particle RNA (right, RF00169) for a p-value threshold of (right, top) and (right, bottom).
The Transat predictions for both RNA families indicate several, mutually incompatible transient helices. In case of the bacterial signal recognition particle, the transient helices (right, bottom, numbered 1–5) are mutually incompatible with the base-pairs of the known structure. The hairpin-like structure of the small nucleolar RNA snR76 seems to fold in one go, whereas the formation of the hairpin-like structure of the bacterial signal recognition particle RNA may first involve the formation of helix 1 which is later replaced by the known hairpin-like structure as the RNA sequence gets further transcribed. Helices 2 to 5 are predicted as statistically more significant (p-values ) than the helices of the known hairpin-like structure. They are mutually exclusive and may correspond to alternative structural confirmations for this sequence. See the text or the caption of Figure 9 for more information on arc-plots.