OPTIMIZING SMITH-WATERMAN ALIGNMENTS

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 delity measure is introduced and shown to capture the signi cance of the local alignment, i.e., the extent to which the correlated subsequences are correctly identi ed. It is demonstrated how the delity may be optimized in the space of penalty parameters using only the alignment score data of a single sequence pair.