A time-efficient, linear-space local similarity algorithm
Advances in Applied Mathematics
On the power of universal bases in sequencing by hybridization
RECOMB '99 Proceedings of the third annual international conference on Computational molecular biology
Sequencing-by-hybridization at the information-theory bound: an optimal algorithm
RECOMB '00 Proceedings of the fourth annual international conference on Computational molecular biology
Better Filtering with Gapped q-Grams
CPM '01 Proceedings of the 12th Annual Symposium on Combinatorial Pattern Matching
Efficient randomized pattern-matching algorithms
IBM Journal of Research and Development - Mathematics and computing
Optimizing Multiple Seeds for Protein Homology Search
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Designing seeds for similarity search in genomic DNA
Journal of Computer and System Sciences - Special issue on bioinformatics II
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
Superiority of Spaced Seeds for Homology Search
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Hardness of optimal spaced seed design
Journal of Computer and System Sciences
Computing Alignment Seed Sensitivity with Probabilistic Arithmetic Automata
WABI '08 Proceedings of the 8th international workshop on Algorithms in Bioinformatics
Amino Acid Classification and Hash Seeds for Homology Search
BICoB '09 Proceedings of the 1st International Conference on Bioinformatics and Computational Biology
Seed optimization for i.i.d. similarities is no easier than optimal Golomb ruler design
Information Processing Letters
New algorithms for the spaced seeds
FAW'07 Proceedings of the 1st annual international conference on Frontiers in algorithmics
A unifying framework for seed sensitivity and its application to subset seeds
WABI'05 Proceedings of the 5th International conference on Algorithms in Bioinformatics
Fast computation of good multiple spaced seeds
WABI'07 Proceedings of the 7th international conference on Algorithms in Bioinformatics
Probabilistic Arithmetic Automata and Their Applications
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
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The novel introduction of spaced seed idea in the filtration stage of sequence comparison by Ma et al. (Bioinformatics 18 (2002) 440) has greatly increased the sensitivity of homology search without compromising the speed of search. Finding the optimal spaced seeds is of great importance both theoretically and in designing better search tool for sequence comparison. In this paper, we study the computational aspects of calculating the hitting probability of spaced seeds; and based on these results, we propose an efficient algorithm for identifying optimal spaced seeds.