Motivation: 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.#R##N##R##N#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.#R##N##R##N#Availability: Source code, executable, data and test results are freely available at ftp://ftp.csiro.au/Horn/RapidMatch#R##N##R##N#Contact: mark.horn@csiro.au#R##N##R##N#Supplementary information:Supplementary data are available at Bioinformatics online.
['Mark E. T. Horn', 'Peter M. Waterhouse']
Rapid match-searching for gene silencing assessment