Figure 5

Quality of similarity detection for profile-based methods of sequence comparison, with different criteria for true positive hits. A. Reference-dependent without consideration of alignment quality. B. Reference-dependent with additional requirement for a minimal alignment quality. C. Reference-independent, global mode. D. Reference-independent, local mode. E. Criteria based on SCOP only: domains in the same superfamily are considered true, domains in different classes are considered false, domains in the same class but different superfamilies or folds are considered 'unknown' and disregarded.