SSAP- Structure and Sequence Alignment Program How about using dynamic programming? Any problems here? 1. How will you evaluate if two positions are similar? Residue type expose to solvent secondary structure relationship to other atoms 2. Score that you give to an alignment of 2 residues depends on other residues alignment depends on SuPeRPosition but SuPeRPOSiTiON depends on ALIGNMENt Taylor, WR, and CA Orengo. " Protein Structure Alignment. J Mol Biol. 208, no. 1 (5 July 1989): 1-22SSAP - Structure and Sequence Alignment Program How about using dynamic programming? Any problems here? 1. How will you evaluate if two positions are similar? Residue type expose to solvent secondary structure relationship to other atoms 2. Score that you give to an alignment of 2 residues depends on other residues ALIGNMENT depends on SUPERPOSITION but SUPERPOSITION depends on ALIGNMENT Taylor, WR, and CA Orengo. "Protein Structure Alignment." J Mol Biol. 208, no. 1 (5 Jul y 1989): 1-22