LecturesPart03

Similarity matrix a a c d e f g h i k l m n p q r s t

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Unformatted text preview: 50 similarity matrix A A C D E F G H I K L M N P Q R S T V W Y C D E F G H I K L M N P Q R S T V W Y 2 -2 0 0 -4 1 -1 -1 -1 -2 -1 0 1 0 -2 1 1 0 -6 -3 -2 12 -5 -5 -4 -3 -3 -2 -5 -6 -5 -4 -3 -5 -4 0 -2 -2 -8 0 0 -5 4 3 -6 1 1 -2 0 -4 -3 2 -1 2 -1 0 0 -2 -7 -4 0 -5 3 4 -5 0 1 -2 0 -3 -2 1 -1 2 -1 0 0 -2 -7 -4 -4 -4 -6 -5 9 -5 -2 1 -5 2 0 -4 -5 -5 -4 -3 -3 -1 0 7 1 -3 1 0 -5 5 -2 -3 -2 -4 -3 0 -1 -1 -3 1 0 -1 -7 -5 -1 -3 1 1 -2 -2 6 -2 0 -2 -2 2 0 3 2 -1 -1 -2 -3 0 -1 -2 -2 -2 1 -3 -2 5 -2 2 2 -2 -2 -2 -2 -1 0 4 -5 -1 -1 -5 0 0 -5 -2 0 -2 5 -3 0 1 -1 1 3 0 0 -2 -3 -4 -2 -6 -4 -3 2 -4 -2 2 -3 6 4 -3 -3 -2 -3 -3 -2 2 -2 -1 -1 -5 -3 -2 0 -3 -2 2 0 4 6 -2 -2 -1 0 -2 -1 2 -4 -2 0 -4 2 1 -4 0 2 -2 1 -3 -2 2 -1 1 0 1 0 -2 -4 -2 1 -3 -1 -1 -5 -1 0 -2 -1 -3 -2 -1 6 0 0 1 0 -1 -6 -5 0 -5 2 2 -5 -1 3 -2 1 -2 -1 1 0 4 1 -1 -1 -2 -5 -4 -2 -4 -1 -1 -4 -3 2 -2 3 -3 0 0 0 1 6 0 -1 -2 2 -4 1 0 0 0 -3 1 -1 -1 0 -3 -2 1 1 -1 0 2 1 -1 -2 -3 1 -2 0 0 -3 0 -1 0 0 -2 -1 0 0 -1 -1 1 3 0 -5 -3 0 -2 -2 -2 -1 -1 -2 4 -2 2 2 -2 -1 -2 -2 -1 0 4 -6 -2 -6 -8 -7 -7 0 -7 -3 -5 -3 -2 -4 -4 -6 -5 2 -2 -5 -6 17 0 -3 0 -4 -4 7 -5 0 -1 -4 -1 -2 -2 -5 -4 -4 -3 -3 -2 0 10 Ala Cys Asp Glu Phe Gly His Ile Lys Leu Met Asn Pro Gln Arg Ser Thr Val Trp Tyr Ala Cys Asp Glu Phe Gly His Ile Lys Leu Met Asn Pro Gln Arg Ser Thr Val Trp Tyr Dayhoff, M., Schwartz, R.M. and Orcutt, B.C. (1978) in: Dayhoff M, ed. Atlas of protein sequence and structure, vol 5 (suppl 3) . Silver Spring, MD: NBRF. 345-352. Dayhoff PAM250 similarity matrix (partial) A A C D E F G H I K L M N C D E F G H I K L M N P 2 -2 0 0 -4 1 -1 -1 -1 -2 -1 0 -2 12 -5 -5 -4 -3 -3 -2 -5 -6 -5 -4 0 -5 4 3 -6 1 1 -2 0 -4 -3 2 0 -5 3 4 -5 0 1 -2 0 -3 -2 1 -4 -4 -6 -5 9 -5 -2 1 -5 2 0 -4 1 -3 1 0 -5 5 -2 -3 -2 -4 -3 0 -1 -3 1 1 -2 -2 6 -2 0 -2 -2 2 -1 -2 -2 -2 1 -3 -2 5 -2 2 2 -2 -1 -5 0 0 -5 -2 0 -2 5 -3 0 1 -2 -6 -4 -3 2 -4 -2 2 -3 6 4 -3 -1 -5 -3 -2 0 -3 -2 2 0 4 6 -2 0 -4 2 1 -4 0 2 -2 1 -3 -2 2 1 -3 -1 -1 -5 -1 0 -2 -1 -3 -2 -1 Origin of PAM 250 matrix s s s s s s s s Take aligned set of closely related proteins For each position in the set, find the most common For amino acid observed there amino Calculate the frequency with which each other Calculate amino acid is observed at that position amino C...
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