title: SWORD-a highly efficient protein database search.
abstract: Protein database search is one of the fundamental problems in bioinformatics. For decades, it has been explored and solved using different exact and heuristic approaches. However, exponential growth of data in recent years has brought significant challenges in improving already existing algorithms. BLAST has been the most successful tool for protein database search, but is also becoming a bottleneck in many applications. Due to that, many different approaches have been developed to complement or replace it. In this article, we present SWORD, an efficient protein database search implementation that runs 8-16 times faster than BLAST in the sensitive mode and up to 68 times faster in the fast and less accurate mode. It is designed to be used in nearly all database search environments, but is especially suitable for large databases. Its sensitivity exceeds that of BLAST for majority of input datasets and provides guaranteed optimal alignments.
  
  
  
  Sword is freely available for download from https://github.com/rvaser/sword
  
  
  
  robert.vaser@fer.hr and mile.sikic@fer.hr
  
  
  
  Supplementary data are available at Bioinformatics online.
authors: Faculty of Electrical Engineering and Computing, University of Zagreb, Unska 3, Zagreb 10000, Croatia.
authors: Robert
authors: R
authors: Vaser
authors: Faculty of Electrical Engineering and Computing, University of Zagreb, Unska 3, Zagreb 10000, Croatia.
authors: Dario
authors: D
authors: Pavlović
authors: Faculty of Electrical Engineering and Computing, University of Zagreb, Unska 3, Zagreb 10000, Croatia Bioinformatics Institute, a*STAR, #07-01 Matrix, 138671, Singapore.
authors: Mile
authors: M
authors: Šikić
mesh_terms: D000465:Algorithms; D030562:Databases, Protein; D057386:Search Engine; D016415:Sequence Alignment; D012984:Software