title: Rapid match-searching for gene silencing assessment.
abstract: BACKGROUND
  Gene silencing, also called RNA interference, requires reliable assessment of silencer impacts. A critical task is to find matches between silencer oligomers and sites in the genome, in accordance with one-to-many matching rules (G-U matching, with provision for mismatches). Fast search algorithms are required to support silencer impact assessments in procedures for designing effective silencer sequences.
  
  
  RESULTS
  The article presents a matching algorithm and data structures specialized for matching searches, including a kernel procedure that addresses a Boolean version of the database task called the skyline search. Besides exact matches, the algorithm is extended to allow for the location-specific mismatches applicable in plants. Computational tests show that the algorithm is significantly faster than suffix-tree alternatives.
  
  
  BACKGROUND
  Source code, executable, data and test results are freely available at ftp://ftp.csiro.au/Horn/RapidMatch.
authors.affiliation: Division of Mathematics, Informatics and Statistics, CSIRO, North Ryde NSW 1670, Australia. mark.horn@csiro.au
authors.forename: Mark E T
authors.initials: ME
authors.lastname: Horn
authors.forename: Peter M
authors.initials: PM
authors.lastname: Waterhouse
mesh_terms: D000465:Algorithms; D030561:Databases, Nucleic Acid; D016678:Genome; D034622:RNA Interference; D022661:RNA, Untranslated / Q000737:chemistry*; D012984:Software
chemical_list: D022661:RNA, Untranslated