An overview of the SFESA method. (A) For each alignment block, SFESA generates up to ±4 variants by shifting (marked as -1, -2, -3, -4, +1, +2, +3, and +4). The pink boxes show the SSEs recognized from template structure and the blue boxes are corresponding regions in the query aligned to such SSEs. Residues and gaps in one corresponding blue and pink boxes compose an alignment block. The corresponding black lines provide the boundaries between which sequence and structure scores are calculated for each aligned residue pairs. (B) If gap shifting is considered, two variants (left and right) are generated by putting gaps on the same side (left or right) before generating the above 8 variants. (C) Flowchart of the SFESA method.