Optimal Group Testing Strategies with Interval Queries and their Application to Splice Site Detection

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.