Consider the two sequence alignments. Alignment 1. A-SNL FDIRLIG GSNDFYEVKIMD Alignment 2. ASNLFDIRLI-G GSNDFYEVKIMD Calculate the alignment scores of each sequence alignment using identity-based scoring and the Blosum-62 substitution matrix. The identity-based scores should incorporate a gap penalty. In this case, the Blosum-62 substitution matrix does not impose a gap penalty. Blosum-62 Substitution Matrix Ala Arg Asn Asp Cys Gin Glu Gly His Ile Leu Lys Met Phe Pro Ser Thr Trp Tyr Val Ala 4 | Arg -1| 5 Asn-2 0 6 | Asp-21-2 1 6 | Cys | 0 |-3 -3 -3 9 Gln-1 1 0 0 -3 5 Glu|-|| 0 0 | 2 -4 2 5 Gly | 0 | 2 | 0 -1 -3 1-2 1-2 6 His -2 | 0 -1 0 0 -2 8 Ile 1-1 -3 -3 -3 -1 -3 | 3 | 4 | 3 | 4 Leu-11-2-3 -4 -1 -2 | 3 | 4 |-3| 2 4 ILys -1| 2 0 -1 -3 1 1 -2-1-3-2 5 Met-1 -1 -2 -3 -1 0 -2-3 1-2 1 2 -1 5 Phe|-21-3 -3 -3 1-2-3-3 1-3 1-1 0 0 -3 0 6 Pro-11-21-2 -1 -3 1-1 1-1 1-2 1-2-3-3 -I -2 -4 7 Ser 1 1 0 -1 0 0 0 -11-21-2 0 -1-2-1 4 Thr 0 0 -1 - -1 -1 -2-2-11-1 -1 - 1-2 1-1 1 5 | Trp|-3-3 -4 -21-2-3-21-2-3-2-3-1 1 -4-3-2 11 | Tyr|-2-2 -2 -2 -2-3 21-11-1 -2 - 1 3 -3-2-2 2 7 Val 0 -3 -3 -3 1-1 -2-2-3 -313 1 -2 1 -1 -21-2 0 -3 - 4 - |--TTTTTTTTT | ||| || - - | - | | | | | | | -1 -1 n|e|||||||| || |-77 -3 What is the alignment score of sequence alignment 1 using identity-based scoring? 1: What is the alignment score of sequence alignment 1 using a Blosum-62 substitution matrix? 1: What is the alignment score of sequence alignment 2 using identity-based scoring? 2: What is the alignment score of sequence alignment 2 using a Blosum-62 substitution matrix? 2: Consider the two sequence alignments. Alignment 1. A-SNL FDIRLIG GSNDFYEVKIMD Alignment 2. ASNLFDIRLI-G GSNDFYEVKIMD Calculate the alignment scores of each sequence alignment using identity-based scoring and the Blosum-62 substitution matrix. The identity-based scores should incorporate a gap penalty. In this case, the Blosum-62 substitution matrix does not impose a gap penalty. Blosum-62 Substitution Matrix Ala Arg Asn Asp Cys Gin Glu Gly His Ile Leu Lys Met Phe Pro Ser Thr Trp Tyr Val Ala 4 | Arg -1| 5 Asn-2 0 6 | Asp-21-2 1 6 | Cys | 0 |-3 -3 -3 9 Gln-1 1 0 0 -3 5 Glu|-|| 0 0 | 2 -4 2 5 Gly | 0 | 2 | 0 -1 -3 1-2 1-2 6 His -2 | 0 -1 0 0 -2 8 Ile 1-1 -3 -3 -3 -1 -3 | 3 | 4 | 3 | 4 Leu-11-2-3 -4 -1 -2 | 3 | 4 |-3| 2 4 ILys -1| 2 0 -1 -3 1 1 -2-1-3-2 5 Met-1 -1 -2 -3 -1 0 -2-3 1-2 1 2 -1 5 Phe|-21-3 -3 -3 1-2-3-3 1-3 1-1 0 0 -3 0 6 Pro-11-21-2 -1 -3 1-1 1-1 1-2 1-2-3-3 -I -2 -4 7 Ser 1 1 0 -1 0 0 0 -11-21-2 0 -1-2-1 4 Thr 0 0 -1 - -1 -1 -2-2-11-1 -1 - 1-2 1-1 1 5 | Trp|-3-3 -4 -21-2-3-21-2-3-2-3-1 1 -4-3-2 11 | Tyr|-2-2 -2 -2 -2-3 21-11-1 -2 - 1 3 -3-2-2 2 7 Val 0 -3 -3 -3 1-1 -2-2-3 -313 1 -2 1 -1 -21-2 0 -3 - 4 - |--TTTTTTTTT | ||| || - - | - | | | | | | | -1 -1 n|e|||||||| || |-77 -3 What is the alignment score of sequence alignment 1 using identity-based scoring? 1: What is the alignment score of sequence alignment 1 using a Blosum-62 substitution matrix? 1: What is the alignment score of sequence alignment 2 using identity-based scoring? 2: What is the alignment score of sequence alignment 2 using a Blosum-62 substitution matrix? 2
