Optimal group testing algorithms with interval queries and their application to splice site detection
by Ferdinando Cicalese, Peter Damaschke, Ugo Vaccaro
International Journal of Bioinformatics Research and Applications (IJBRA), Vol. 1, No. 4, 2005

Abstract: Given an ordered set of n items and an unknown subset P of up to p positive elements, we want to identify P by asking the least number of queries 'does Q intersect P?' where Q must consist of consecutive elements. This Interval Group Testing problem arises in the context of splice site detection in genes. We study algorithms that operate in a few stages where queries chosen depending on previous answers, are performed in parallel. We obtain tight bounds for two-stage strategies. Finally, we get results for any number of stages and positives.

Online publication date: Tue, 20-Dec-2005

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