Transat—A Method for Detecting the Conserved Helices of Functional RNA Structures, Including Transient, Pseudo-Knotted and Alternative Structures
For several Rfam families, the Transat predictions propose a pseudo-knotted configuration, see the S-adenosyl-L-homocysteine ribo-switch (left, top, RF01057), the glmS glucosamine-6-phosphate activated ribozyme (left, bottom, RF00234), the small nucleolar RNA U3 (right, top, RF00012) and the U12 minor spliceosomal RNA (right, bottom, RF00007).
For a p-value threshold of , Transat predicts the helices of the known structures correctly and also provides strong statistical evidence (p-value ) for additional helices that would render the known secondary structure pseudo-knotted, see the blue bottom-arcs for all four RNA families. Note that for the U12 minor spliceosomal RNA (right, bottom), the newly predicted helix is in competition with the most 5′ helix that is part of the known RNA secondary structure. See the text or the caption of Figure 9 for more information on arc-plots.