SOV_refine is a refined definition of segment overlap score based on the previous definitons of SOV scores (SOV'99) (Zemla, A. et al., 1999, proteins) and (SOV'94) (Rost, B. et al., 1994, J. Mol. Biol.), which were initially designed to evaluate the quality of protein secondary structure predictions. SOV_refine redefined the assignment of allowance in SOV'99, which can ensure that the amount of allowance is incremental when one more element in the predicted sequence is further predicted accurately.
SOV scores (SOV'99 and SOV_refine) can be used in all sequence similarity comparison especially for those sequences with multiple overlapping segments.
Source code can be downloaded here. The perl script "SOV_refine.pl" can generate accuracy (e.g., Q3), SOV'99, and SOV_refine scores.
Tong Liu and Zheng Wang. SOV_refine: A further refined definition of segment overlap score and its significance for protein structure similarity. Source Code for Biology and Medicine,(2018) 13:1.