On the closest string and substring problems
Journal of the ACM (JACM)
Computers and Intractability: A Guide to the Theory of NP-Completeness
Computers and Intractability: A Guide to the Theory of NP-Completeness
Designing seeds for similarity search in genomic DNA
RECOMB '03 Proceedings of the seventh annual international conference on Research in computational molecular biology
ESA '99 Proceedings of the 7th Annual European Symposium on Algorithms
Designing multiple simultaneous seeds for DNA similarity search
RECOMB '04 Proceedings of the eighth annual international conference on Resaerch in computational molecular biology
Sensitivity analysis and efficient method for identifying optimal spaced seeds
Journal of Computer and System Sciences
On spaced seeds for similarity search
Discrete Applied Mathematics
Estimating Seed Sensitivity on Homogeneous Alignments
BIBE '04 Proceedings of the 4th IEEE Symposium on Bioinformatics and Bioengineering
Efficient Methods for Generating Optimal Single and Multiple Spaced Seeds
BIBE '04 Proceedings of the 4th IEEE Symposium on Bioinformatics and Bioengineering
Good spaced seeds for homology search
Bioinformatics
Hardness of optimal spaced seed design
CPM'05 Proceedings of the 16th annual conference on Combinatorial Pattern Matching
Hardness of optimal spaced seed design
Journal of Computer and System Sciences
Seed optimization for i.i.d. similarities is no easier than optimal Golomb ruler design
Information Processing Letters
MPSCAN: fast localisation of multiple reads in genomes
WABI'09 Proceedings of the 9th international conference on Algorithms in bioinformatics
Spaced seeds design using perfect rulers
SPIRE'11 Proceedings of the 18th international conference on String processing and information retrieval
Design and analysis of periodic multiple seeds
Theoretical Computer Science
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Optimal spaced seeds were introduced by the theoretical computer science community to bioinformatics to effectively increase homology search sensitivity. These seeds are serving many homology queries daily. However the computational complexity of finding the optimal spaced seeds remains to be open. In this paper, we prove that computing hit probability of a spaced seed in a uniform homology region is NP-hard, but it admits a probabilistic PTAS. We also show that the asymptotic hit probability is computable in exponential time in seed length, independent of the homologous region length.