title: Good spaced seeds for homology search.
abstract: BACKGROUND
  Filtration is an important technique used to speed up local alignment as exemplified in the BLAST programs. Recently, Ma et al. discovered that better filtering can be achieved by spacing out the matching positions according to a certain pattern, instead of contiguous positions to trigger a local alignment in their PatternHunter program. Such a match pattern is called a spaced seed.
  
  
  RESULTS
  Our numerical computation shows that the ranks of spaced seeds (based on sensitivity) change with the sequences similarity. Since homologous sequences may have diverse similarity, we assess the sensitivity of spaced seeds over a range of similarity levels and present a list of good spaced seeds for facilitating homology search in DNA genomic sequences. We validate that the listed spaced seeds are indeed more sensitive using three arbitrarily chosen pairs of DNA genomic sequences.
authors.affiliation: Department of Mathematics, National University of Singapore, Singapore 117543. matzlx@nus.edu.sg
authors.forename: Kwok Pui
authors.initials: KP
authors.lastname: Choi
authors.forename: Fanfan
authors.initials: F
authors.lastname: Zeng
authors.forename: Louxin
authors.initials: L
authors.lastname: Zhang
mesh_terms: D000465:Algorithms; D000818:Animals; D002874:Chromosome Mapping / Q000379:methods*; D004926:Escherichia coli / Q000235:genetics; D020869:Gene Expression Profiling / Q000379:methods; D051379:Mice; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012689:Sequence Homology, Nucleic Acid