Abstract
The (l,d)-motif challenge problem, as introduced by Pevzner and Sze, is a mathematical abstraction of the DNA functional site discovery task. Here we expand the (l,d)-motif problem to more accurately model this task and present a novel algorithm to solve this extended problem. This algorithm is guaranteed to find all (l,d)-motifs in a set of input sequences with unbounded support and length. We demonstrate the performance of the algorithm on publicly available datasets and show that the algorithm deterministically enumerates the optimal motifs.
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