Cyclotide Structure–Activity Relationships: Qualitative and Quantitative Approaches Linking Cytotoxic and Anthelmintic Activity to the Clustering of Physicochemical Forces
Figure 4
Template selection strategy based on the NJ tree.
This figure illustrates the strategy of a template selection using a cladogram in which the target sequence (a) relates differently to various sequences of known structure. The symbols R and R′ represent the other branches of the cladograms. These branches contain sequences of known structure. Our aim was to identify sequences of known structure that could reasonably be used as templates for the target sequence based on the bootstrapped consensus tree. The procedure used to select the template sequences most closely related to the target sequence from the bootstrap NJ tree depended on the structure of the tree and the position of the target sequence relative to the nearest neighbors of known structure. In cases such as that shown in subfigure A, a single peptide of known structure (b) was selected as the template for target sequence (a) if the bootstrap value for the two taxa, a and b, was greater than 50%. Two taxa, b and c were selected if the bootstrap value for taxa a and b was below 50%. In cases such as that shown in subfigure B, two taxa, b and c were selected as templates, regardless of the bootstrap value of the common ancestor of the three taxa, a, b and c. In case C, we randomly chose two templates from the sister taxa (R′) of the target sequence (a) if the sister taxa (R′) included two or more sequences of known structure.