Fast Practical Exact and Approximate Pattern Matching in Protein Sequences
C.S. Iliopoulos, Inuka Jayasekera, Laurent Mouchard · 2006
Abstract. Here we design, analyse and implement an algorithm that searches for motifs in protein sequences using masking techniques (“wordlevel” parrallelism). Our algorithm speeds up known algorithms by a factor of 20 (or the alphabet size). Furthermore, we present graphs of the running times of the algorithm in comparison to its theoritical time complexity.