Structural DNA profiles: single sequence queries

Structural DNA profiles use the structural properties of the constituent octamers either to observe any characteristics of a single sequence that are unusual (a single sequence query) or to visualize a pattern common to a set of sequences (a multiple sequence query). They are an aid in understanding structural reasons for functional DNA activity. Profiles that answer single sequence queries are introduced and Profile Manager (a software application developed to automate profile generation) is presented. Two sequences that are similar by their nucleotide composition but are known to be very different by structure are analyzed, resulting in useful illustrations that agree with the experimental nuclear magnetic resonance structures.