Finding motifs using random projections
RECOMB '01 Proceedings of the fifth annual international conference on Computational biology
Finding similar regions in many sequences
Journal of Computer and System Sciences - STOC 1999
Combinatorial Approaches to Finding Subtle Signals in DNA Sequences
Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology
On the Structure of Small Motif Recognition Instances
SPIRE '08 Proceedings of the 15th International Symposium on String Processing and Information Retrieval
Why large CLOSEST STRING instances are easy to solve in practice
SPIRE'10 Proceedings of the 17th international conference on String processing and information retrieval
New bounds for motif finding in strong instances
CPM'06 Proceedings of the 17th Annual conference on Combinatorial Pattern Matching
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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 practice. However, the previously known bounds on its performance are useless when runtimes are actually manageable. Here, we present much sharper lower and upper bounds on the performance of this algorithm that partially explain why its behavior is so much better in practice than what was previously predicted in theory. We also give specific examples of instances of the problem for which the PTAS performs poorly in practice, and show that the asymptotic performance bound given in the original proof matches the behaviour of a simple variant of the algorithm on a particularly bad instance of the problem.