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In 2003, Gusfield introduced the Haplotype Inference by Pure Parsimony (HIPP) problem and presented an integer program (IP) that quickly solved many simulated instances of the problem [1]. Although it solved well on small instances, Gusfield's IP can be of exponential size in the worst case. Several authors [2], [3] have presented polynomial-sized IPs for… (More)

Many algorithms for motif finding that are commonly used in bioinformatics start by sampling r potential motif occurrences from n input sequences. The motif is derived from these samples and evaluated on all sequences. This approach works extremely well in practice, and is implemented by several programs. Li, Ma and Wang have shown that a simple algorithm… (More)

Haplotype inference by pure parsimony (HIPP) is known to be NP-Hard. Despite this, many algorithms successfully solve HIPP instances on simulated and real data. In this paper, we explore the connection between algebraic rank and the HIPP problem, to help identify easy and hard instances of the problem. The rank of the input matrix is known to be a lower… (More)

We present sharper upper and lower bounds for a known polynomial-time approximation scheme due to Li, Ma and Wang [7] for the Consensus-Pattern problem. This NP-hard problem is an abstraction of motif finding, a common bioinformatics discovery task. The PTAS due to Li et al. is simple, and a preliminary implementation [8] gave reasonable results in… (More)

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