Alignments without low-scoring regions

  title={Alignments without low-scoring regions},
  author={Zheng Zhang and Piotr Berman and Webb Miller},
  journal={Journal of computational biology : a journal of computational molecular cell biology},
  volume={5 2},
Given a strong match between regions of two sequences, how far can the match be meaningfully extended if gaps are allowed in the resulting alignment? The aim is to avoid searching beyond the point that a useful extension of the alignment is likely to be found. Without loss of generality, we can restrict attention to the suffixes of the sequences that follow the strong match, which leads to the following formal problem. Given two sequences and a fixed X > 0, align initial portions of the… CONTINUE READING

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