Question: Question #2 (total 30 points): Align the following two sequences using the dynamic programming method. Use Blosum 62 as the similarity matrix (see table 1).
Question #2 (total 30 points): Align the following two sequences using the "dynamic programming method". Use Blosum 62 as the similarity matrix (see table 1). The gap penalty is -5 for both gap opening and gap extension. Draw the matrix with scores and paths. Write the final alignment and the final score. >protein_x VDSCY >protein_y VESLCY Snowo Table 1. BLOSUM62 Matrix Ala 4 Arg - 15 Asn -2 0 6 Asp -2 -2 1 6 Cys 0 -3 -3 -3 9 Gin - 1 1 0 0 -3 5 Glu . 1 0 0 2 .4 2 5 Gly 0 - 2 0 -1 -3 -2 -2 6 His - 2 0 1 -1 -3 0 0 - 2 8 lle -1 -3 -3 -3 -1 -3 -3 -4 -3 4 Leu -1 -2 -3 -4 -1 -2 -3 -4 -3 2 4 Lys -1 2 0 -1 -3 1 1 -2 -1 -3 -2 5 Met -1 -1 -2 -3 -1 0 -2 -3 -2 1 2 -1 5 Phe -2 -3 -3 -3 -2 -3 -3 -3 - 1 0 0 3 0 6 Pro -1 -2 -2 -1 -3 -1 -1 -2 -2 -3 -3 -1 -2 -4 7 Ser 1 - 1 1 0 -1 0 0 0 -1 -2 -2 0 -1 -2 -1 4 Thr 0 - 1 0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -2 -1 1 5 Trp .3 .3 .4 .4 -2 -2 -3 -2 -2 -3 -2 -3 - 1 1 -4 -3 -2 11 Tyr 1 -2 -2 -2 -3 -2 -1 -2 -3 2 -1 -1 -2 -1 3 -3 -2 -2 2 7 Val 0 -3 -3 -3 -1 -2 -2 -3 -3 3 1 - 2 1 -1 -2 -2 0 -3 1 4 Ala Arg Asn Asp Cys Gin Glu Gly His lle Leu Lys Met Phe Pro Ser Thr Trp Tyr Val Question #2 (total 30 points): Align the following two sequences using the "dynamic programming method". Use Blosum 62 as the similarity matrix (see table 1). The gap penalty is -5 for both gap opening and gap extension. Draw the matrix with scores and paths. Write the final alignment and the final score. >protein_x VDSCY >protein_y VESLCY Snowo Table 1. BLOSUM62 Matrix Ala 4 Arg - 15 Asn -2 0 6 Asp -2 -2 1 6 Cys 0 -3 -3 -3 9 Gin - 1 1 0 0 -3 5 Glu . 1 0 0 2 .4 2 5 Gly 0 - 2 0 -1 -3 -2 -2 6 His - 2 0 1 -1 -3 0 0 - 2 8 lle -1 -3 -3 -3 -1 -3 -3 -4 -3 4 Leu -1 -2 -3 -4 -1 -2 -3 -4 -3 2 4 Lys -1 2 0 -1 -3 1 1 -2 -1 -3 -2 5 Met -1 -1 -2 -3 -1 0 -2 -3 -2 1 2 -1 5 Phe -2 -3 -3 -3 -2 -3 -3 -3 - 1 0 0 3 0 6 Pro -1 -2 -2 -1 -3 -1 -1 -2 -2 -3 -3 -1 -2 -4 7 Ser 1 - 1 1 0 -1 0 0 0 -1 -2 -2 0 -1 -2 -1 4 Thr 0 - 1 0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -2 -1 1 5 Trp .3 .3 .4 .4 -2 -2 -3 -2 -2 -3 -2 -3 - 1 1 -4 -3 -2 11 Tyr 1 -2 -2 -2 -3 -2 -1 -2 -3 2 -1 -1 -2 -1 3 -3 -2 -2 2 7 Val 0 -3 -3 -3 -1 -2 -2 -3 -3 3 1 - 2 1 -1 -2 -2 0 -3 1 4 Ala Arg Asn Asp Cys Gin Glu Gly His lle Leu Lys Met Phe Pro Ser Thr Trp Tyr Val
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