Rapid match-searching for gene silencing assessment.

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. 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. AVAILABILITY: Source code, executable, data and test results are freely available at ftp://ftp.csiro.au/Horn/RapidMatch.

Measures of societal risk and their potential use in civil aviation.

This article seeks to clarify the conceptual foundations of measures of societal risk, to investigate how such measures may be used validly in commonly encountered policy contexts, and to explore the application of these measures in the field of civil aviation. The article begins by examining standard measures of societal and individual risk (SR and IR), with attention given to ethical as well as analytical considerations. A comprehensive technical analysis of SR is provided, encompassing scalar risk measures, barrier functions, and a utility-based formulation, and clarifications are offered with respect to the treatment of SR in recent publications. The policy context for SR measures is shown to be critically important, and an extension to a hierarchical setting is developed. The prospects for applying SR to civil aviation are then considered, and some technical and conceptual issues are identified. SR appears to be a useful analytical tool in this context, provided that careful attention is given to these issues.