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Alignment quality for profile-based methods of sequence comparison. Reference-dependent parameters (Qdeveloper (A), Qmodeller (B), coverage (C), Qlocal (D)) and reference-independent parameters (original GDT_TS (E) and local GDT_TS version (F)) are compared for PSI-BLAST, COMPASS, prof_ss, and HHsearch versions with and without consideration of predicted secondary structure, for several bins of sequence identity.
