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Figure 7 | BMC Bioinformatics

Figure 7

From: R2R - software to speed the depiction of aesthetic consensus RNA secondary structures

Figure 7

Multistem-junction layout as a non-linear program. (A) Illustration of first formulation, with circle drawn. The unpaired nucleotides on the junction (blue circles) perfectly fit the circle by construction, while the paired nucleotides (green circles) do not. The purple line indicates the angle of the nucleotide 5' to the enclosing pair, whose optimal value is roughly 58°. (B) The line connecting two paired nucleotides is shown in purple, and different intersection points are shown, from 5' nucleotide (i = 0) to 3' (i = 1). The optimal value is roughly i = 0.3. (C) Two purple lines mark the distance dn from the circle's center to a base-paired nucleotide, and da from the circle's center to the adjacent nucleotide. Each of the four base-paired nucleotides in this example will contribute a term (dn-da)2 to the objective function. (D) Illustration of second formulation, using an example chosen so that some nucleotides would deviate significantly from the main circle. This circle is again shown explicitly. (E) The lower right unpaired region deviates from the main circle, but is positioned along an independent circle, which is shown. The four purple lines indicate deviations from this independent circle to the target main circle. Each of these lines corresponds to a term in the objective function.

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