Superiority and complexity of the spaced seeds

@inproceedings{Li2006SuperiorityAC,
  title={Superiority and complexity of the spaced seeds},
  author={Ming Li and Bin Ma and Louxin Zhang},
  booktitle={SODA},
  year={2006}
}
Optimal spaced seeds were introduced by the theoretical computer science community to bioinformatics to effectively increase homology search sensitivity. They are now serving thousands of homology search queries daily. While dozens of papers have been published on optimal spaced seeds since their invention, many fundamental questions still remain unanswered. In this paper, we settle several open questions in this area. Specifically, we prove that when the length of a non-uniformly spaced seed… CONTINUE READING

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