Better filtering with gapped q-grams
Fundamenta Informaticae - Special issue on computing patterns in strings
On spaced seeds for similarity search
Discrete Applied Mathematics
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
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
Journal of Computer and System Sciences
ZOOM! Zillions of oligos mapped
Bioinformatics
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We consider the problem of lossless spaced seed design for approximate pattern matching. We show that, using mathematical objects known as perfect rulers, we can derive a family of spaced seeds for matching with up to two errors. We analyze these seeds with respect to the trade-off they offer between seed weight and the minimum length of the pattern to be matched. We prove that for patterns of length up to a few hundreds our seeds have a larger weight, hence a better filtration efficiency, than the ones known in the literature. In this context, we study in depth the specific case of Wichmann rulers and prove some preliminary results on the generalization of our approach to the larger class of unrestricted rulers.