Transat—A Method for Detecting the Conserved Helices of Functional RNA Structures, Including Transient, Pseudo-Knotted and Alternative Structures
The helices of the pseudo-knotted known structure for the bacterial tmRNA are correctly predicted by Transat. Transat also predicts several additional helices, but the region of the tmRNA sequences that contains the reading frame which ends in a translation stop signal is devoid of statistically significant transient helices supporting the hypothesis that the sequence in this region in the 5′ half of the RNA has been chosen to remain single-stranded and readily accessible. RNAalifold P predicts only a few of the helices of the known pseudo-knotted structure and no additional structural features, see also Figure 15. Please refer to the caption of Figure 16 for more information on arc-plots.