title: SW#-GPU-enabled exact alignments on genome scale.
abstract: CONCLUSIONS
  We propose SW#, a new CUDA graphical processor unit-enabled and memory-efficient implementation of dynamic programming algorithm, for local alignment. It can be used as either a stand-alone application or a library. Although there are other graphical processor unit implementations of the Smith-Waterman algorithm, SW# is the only one publicly available that can produce sequence alignments on genome-wide scale. For long sequences, it is at least a few hundred times faster than a CPU version of the same algorithm.
  
  
  BACKGROUND
  Source code and installation instructions freely available for download at http://complex.zesoi.fer.hr/SW.html.
authors.affiliation: Faculty of Electrical Engineering and Computing, University of Zagreb, Unska 3, HR 10000 Zagreb, Croatia and Bioinformatics Institute, A*STAR, #07-01 Matrix, 138671 Singapore.
authors.forename: Matija
authors.initials: M
authors.lastname: Korpar
authors.forename: Mile
authors.initials: M
authors.lastname: Šikic
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D016678:Genome; D020407:Internet; D016415:Sequence Alignment; D012984:Software