Optimal group testing algorithms with interval queries and their application to splice site detection

Authors:
Ferdinando Cicalese;Peter Damaschke;Ugo Vaccaro
Affiliations:
Institute of Bioinformatics, Center of Biotechnology (CeBiTec), Bielefeld University, 33594 Bielefeld, Germany.;School of Computer Science and Engineering, Chalmers University, 41296 Goteborg, Sweden.;Department of Computer Science and Applications, University of Salerno, 84081 Baronissi (SA), Italy
Venue:
International Journal of Bioinformatics Research and Applications
Year:
2005

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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.