title: Seeds for effective oligonucleotide design.
abstract: BACKGROUND
  DNA oligonucleotides are a very useful tool in biology. The best algorithms for designing good DNA oligonucleotides are filtering out unsuitable regions using a seeding approach. Determining the quality of the seeds is crucial for the performance of these algorithms.
  
  
  RESULTS
  We present a sound framework for evaluating the quality of seeds for oligonucleotide design. The F - score is used to measure the accuracy of each seed. A number of natural candidates are tested: contiguous (BLAST-like), spaced, transitions-constrained, and multiple spaced seeds. Multiple spaced seeds are the best, with more seeds providing better accuracy. Single spaced and transition seeds are very close whereas, as expected, contiguous seeds come last. Increased accuracy comes at the price of reduced efficiency. An exception is that single spaced and transitions-constrained seeds are both more accurate and more efficient than contiguous ones.
  
  
  CONCLUSIONS
  Our work confirms another application where multiple spaced seeds perform the best. It will be useful in improving the algorithms for oligonucleotide design.
authors.affiliation: Department of Computer Science, University of Western Ontario, London, ON, Canada. ilie@csd.uwo.ca
authors.forename: Lucian
authors.initials: L
authors.lastname: Ilie
authors.forename: Silvana
authors.initials: S
authors.lastname: Ilie
authors.forename: Shima
authors.initials: S
authors.lastname: Khoshraftar
authors.forename: Anahita Mansouri
authors.initials: AM
authors.lastname: Bigvand
mesh_terms: D004247:DNA / Q000235:genetics; D021141:Nucleic Acid Amplification Techniques / Q000379:methods*; D009841:Oligonucleotides / Q000235:genetics*
chemical_list: D009841:Oligonucleotides; D004247:DNA