Figure 1

The NASSAM pseudoatom vectors and pattern matrix system. (A) Example of a base triple composed of a guanine (Base 1), a cytosine (Base 2) and another guanine (Base 3). The pseudoatom nodes used to set the distances for the pattern matrix have been marked with Sx, Ex and Ey while the distances between these nodes have been marked with arrows. (B) An example set of vectors and their corresponding distances (in Angstroms) which define the GGC triple orientation in section (A). (C) The corresponding pattern matrix file built from the vectors (distances X10) defined in section (B) for the triple pattern shown in section (A). As an example, the SxSx distance between Base 1 and Base 3 is 10Ǻ and is marked 100 under the SS column where Base 1, Node X and Base 3, Node X intersect.