Implementation of the Vectorized Position-Specic Iterated Smith-Waterman Algorithm with Heuristic Filtering Algorithm on Cray Architecture
Witold Remigiusz Rudnicki, Rafal Maszkowski, Łukasz Bolikowski, Maciej Cytowski, Maciej Dobrzynski, Maria Fronczak · 2005
Smith-Waterman is the algorithm for nding local optimal alignments of two amino acid sequences, but is too slow for use in regular large database scanning. We have implemented SW algorithm on Cray X1 architecture, exploiting vectorization and parallelization. In addition we have proposed heuristic database ltering algorithm, which is particularly well suited for the Cray architecture, exploiting possibilities given by the BMM unit.