Description of SEA program variants and other programs
SEA_ssi: local structures derived from 3D structures are exploited by SEA
SEA_c30: up to 30 local structure segments (LSSs) are allowed for each position
SEA_1d: one-dimensional predicted local structures are exploited by SEA
FFAS: the profile-profile sequence alignment
CE: the structural alignment
The measures of alignment accuracy
The root mean square deviation (RMSD) of C-alpha positions after optimal superposition
Shift score (Cline et al., 2002). The shift score measures misalignment between a predicted alignment of two proteins and their reference alignment, which is often a structural alignment; it ranges from -epsilon (default as -0.2) and 1.0, where 1.0 means an identical alignment.