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

Figure 9

Conserved helices predicted by Transat for the hok data set for different p-value threshold values (left , right ).

The x-axis represents the hok alignment. Each arc corresponds to a base-pair between the respective positions in the alignment. Arcs above the x-axis correspond to known base-pairs, whereas arcs below correspond to new base-pairs predicted by Transat, i.e. they correspond to base-pairs that do not involve the same pair of nucleotide positions as any base-pair in the known structure(s). Base-pairs predicted by Transat have non-black colours which indicate their reliability as estimated by Transat ( green, blue, orange and (p-value threshold) red). They can either be found above the x-axis, if they agree with a pair in the reference structure(s), or below, if they are new. Transat predicts most helices of the known structure as well as three statistically significant conserved helices which may guide the structure formation.

Figure 9