An efficient and high performance linear recursive variable expansion implementation of the Smith-Waterman algorithm.
In this paper, we present an efficient and high performance linear recursive variable expansion (RVE) implementation of the Smith-Waterman (S-W) algorithm and compare it with a traditional linear systolic array implementation. The results demonstrate that the linear RVE implementation performs up to 2.33 times better than the traditional linear systolic array implementation, at the cost of utilizing 2 times more resources.
Hasan
Laiq
L
Delft University of Technology,The Netherlands. L.HASAN@EWI.TUDELFT.NL
Al-Ars
Zaid
Z
D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D003196:Computer Graphics; D003201:Computers; D004867:Equipment Design; D006801:Humans; D016247:Information Storage and Retrieval; D015203:Reproducibility of Results; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000295:instrumentation*; D020539:Sequence Analysis, Protein / Q000295:instrumentation*; D012815:Signal Processing, Computer-Assisted; D012984:Software