Construction of the full local similarity map for two biopolymers.

A novel algorithm for construction of complete maps of local similarity for two biopolymer sequences is described. The algorithm is much faster than the related Altschul-Erickson procedure, it is implemented as the Dot-Helix module within the GeneBee package. Performance of the algorithm is exemplified with the analysis of the polyproteins of two poliovirus type 3 strains and its effectivity is compared to the Staden method. Possible applications of the algorithm are briefly discussed.