Rapid match-searching for gene silencing assessment.
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.
Horn
Mark E T
ME
Division of Mathematics, Informatics and Statistics, CSIRO, North Ryde NSW 1670, Australia. mark.horn@csiro.au
Waterhouse
Peter M
PM
D000465:Algorithms; D030561:Databases, Nucleic Acid; D016678:Genome; D034622:RNA Interference; D022661:RNA, Untranslated / Q000737:chemistry*; D012984:Software
D022661:RNA, Untranslated