ON ALIGNMENT SHIFT AND ITS MEASURES
Melissa Cline, Kevin J. Karplus · 1998
This document proposes a new measure for comparing two alignments, referred to as the shift score. This score has a range of -epsilon to 1, where epsilon is a small number used as a parameter to the scoring algorithm. A score of 1 is attained only if the two alignments are identical. The shift score is symmetric with respect to the alignments - no distinguished sequence or alignment is needed. The score incorporates both coverage measures and shift error measures into a single number. The shift score is easily computed, and one can find the optimum subalignment of a candidate alignment (the subalignment that maximizes the shift score) with a simple greedy algorithm.