All hits all the time: parameter-free calculation of spaced seed sensitivity

@article{Mak2009AllHA,
  title={All hits all the time: parameter-free calculation of spaced seed sensitivity},
  author={Denise Y. F. Mak and Gary Benson},
  journal={Bioinformatics},
  year={2009},
  volume={25 3},
  pages={302-8}
}
MOTIVATION Standard search techniques for DNA repeats start by identifying small matching words, or seeds, that may inhabit larger repeats. Recent innovations in seed structure include spaced seeds and indel seeds which are more sensitive than contiguous seeds. Evaluating seed sensitivity requires (i) specifying a homology model for alignments and (ii) assigning probabilities to those alignments. Optimal seed selection is resource intensive because all alternative seeds must be tested. Current… CONTINUE READING
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