Figure 1.

Algorithms for primer self-complementarity (primerSelfcom) and cross hybridization (primerDimers) computing. (a), (b) and (c) show three stages of the sliding window triplet extraction step. All the DNA string is reduced into overlapping triplets. (d) reflects the general overview of the algorithm. As a first step, triplets are extracted for each primer. Then, primers are reverse complemented and thereafter splitted into overlapping triplets. Comparison between triplets allows the generation of an estimate of similarity, which is employed as a hybridization predictor.