Optimizing Smith-Waterman alignments

Details Optimizing Smith-Waterman alignments Optimizing Smith-Waterman alignments

1998-11-16

arxiv.org/abs/cond-mat/9811225v1

Physics

Condensed Matter

12 pages, 5 figures

Scientific paper

Mutual correlation between segments of DNA or protein sequences can be detected by Smith-Waterman local alignments. We present a statistical analysis of alignment of such sequences, based on a recent scaling theory. A new fidelity measure is introduced and shown to capture the significance of the local alignment, i.e., the extent to which the correlated subsequences are correctly identified. It is demonstrated how the fidelity may be optimized in the space of penalty parameters using only the alignment score data of a single sequence pair.

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