Designing seeds for similarity search in genomic DNA
RECOMB '03 Proceedings of the seventh annual international conference on Research in computational molecular biology
Better Filtering with Gapped q-Grams
CPM '01 Proceedings of the 12th Annual Symposium on Combinatorial Pattern Matching
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
Efficient Methods for Generating Optimal Single and Multiple Spaced Seeds
BIBE '04 Proceedings of the 4th IEEE Symposium on Bioinformatics and Bioengineering
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Good spaced seeds for homology search
Bioinformatics
Superiority and complexity of the spaced seeds
SODA '06 Proceedings of the seventeenth annual ACM-SIAM symposium on Discrete algorithm
On the complexity of the spaced seeds
Journal of Computer and System Sciences
Optimal spaced seeds for faster approximate string matching
Journal of Computer and System Sciences
Hardness of optimal spaced seed design
CPM'05 Proceedings of the 16th annual conference on Combinatorial Pattern Matching
A class of binary recurrent codes with limited error propagation
IEEE Transactions on Information Theory
Fast computation of good multiple spaced seeds
WABI'07 Proceedings of the 7th international conference on Algorithms in Bioinformatics
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The spaced seed is a filtration method to efficiently identify the regions of interest in string similarity searches. It is important to find the optimal spaced seed that achieves the highest search sensitivity. For some simple distributions of the similarities, the seed optimization problem was proved to be not NP-hard. On the other hand, no polynomial time algorithm has been found despite the extensive researches in the literature. In this article we examine the hardness of the seed optimization problem by a polynomial time reduction from the optimal Golomb ruler design problem, which is a well-known difficult (but not NP-hard) problem in combinatorial design.