title: Fast computation of neighbor seeds.
abstract: BACKGROUND
  Alignment of biological sequences is one of the most frequently performed computer tasks. The current state of the art involves the use of (multiple) spaced seeds for producing high quality alignments. A particular important class is that of neighbor seeds which combine high sensitivity with reduced space requirements. Current algorithms for computing good neighbor seeds are very slow (exponential).
  
  
  RESULTS
  We give a polynomial-time heuristic algorithm that computes better neighbor seeds than previous ones while being several orders of magnitude faster.
authors.affiliation: Department of Computer Science, University of Western Ontario, London N6A 5B7, Ontario, Canada. ilie@csd.uwo.ca
authors.forename: Lucian
authors.initials: L
authors.lastname: Ilie
authors.forename: Silvana
authors.initials: S
authors.lastname: Ilie
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D016415:Sequence Alignment / Q000379:methods*