Figure 5

The simplified dependency structure found in the data from Figure1, and shown in Figure3, cast into the biological context of the molecular family from which the data was derived. The aligned PSSM and interpositional dependencies for a sequence family identified by MAVL/StickWRLD correspond to a GPM where each possible base in each position represents to a node, and dependencies form edges. In this representation of a portion of the endonuclease target, the color of each node represents the base identity, and the size represents the frequency distribution of that base at that location in the sequence. Important positive dependencies are shown as black edges, and important negative dependencies are shown as dashed light-red edges. The “X shaped” dependencies in the lower stem correspond to the Watson-Crick interactions of a stem-loop structure. The dependencies within the bulge, and between the central stem and the bulge, are non-Watson-Crick, and are completely lost by other modeling methods. A few additional edges that are implied by the data are shown here, that could not be shown without overly cluttering Figure 3. Fundamentally, the universal domain need is for a method of producing figures with similar information, without the need for significant manual intervention.