Overview of nucleic acid analysis programs

We outline the mathematical distinctions among seven of the most popular co mputer programs currently used to analyze the spatial arrangements of bases and base pairs in nucleic acid helical structures. The schemes fall into t hree basic categories on the basis of their definitions of rotational param eters: matrix-based, projection-based, and combined matrix- and projection- based. The approaches also define and construct base and base-pair coordina te frames in a variety of ways. Despite these mathematical distinctions, th e computed parameters from some programs are strongly correlated and direct ly comparable. By contrast, other programs which use identical methodologie s sometimes yield very different results. The choice of reference frame rat her than the mathematical formulation has the greater effect on calculated parameters. Any factor which influences the reference frame, such as fittin g or not fitting standard bases to the experimentally derived coordinates, will have a noticeable effect on both complementary base pair and dimer ste p parameters.