Physical Sciences and Mathematics Commons^™

A New Approach To Sequence Local Alignment: Normalization With Concave Functions, Qiang Zhou

Electronic Thesis and Dissertation Repository

Sequence local alignment is to find two subsequences from the input two sequences respectively, which can produce the highest similarity degree among all other pairs of subsequences. The Smith-Waterman algorithm is one of the most important technique in sequence local alignment, especially in computational molecular biology. This algorithm can guarantee that the optimal local alignment can be found with respect to the distance or similarity metric. However, the optimal solution obtained by Smith-Waterman is not biologically meaningful, since it may contain small pieces of irrelevant segments, but as long as they are not strong enough, the algorithm still take them …