mg640Seqs - PROTEIN SEQUENCE COMPARISONS SEQUENCE...

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SEQUENCE COMPARISONS PROTEIN SEQUENCE COMPARISONS compare the number of amino acid differences 10 of 18 a.a. sites have differences γ -interferon signal peptide protein sequence comparisons compare the number of amino acid differences example: gamma interferon signal peptide of human and mouse: 10 / 18 sites are different model assume that amino acid changes occur at a rate λ per unit time two independently evolving lineages, initially identical in sequence at time t there are a proportion D t differences Model of sequence divergence
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Poisson correction (PC) model assume that amino acid changes occur at a rate λ per unit time two independently evolving lineages, initially identical in sequence at time t there are a proportion D t differences at time t + 1 D (t+1) = (1 - D t ) (2 λ ) + D t assume that amino acid changes occur at a rate λ per unit time D (t+1) = (1 - D t ) (2 λ ) + D t D t = 1 - e -2 λ t expected proportion of difference, K a K a = 2 λ t or K a = -ln ( 1 - D) Poisson correction (PC) model assume that amino acid changes occur at a rate λ per unit time total number of amino acid substitutions per site (expected proportion of differences) K a = 2 λ t or K a = -ln ( 1 – D ) and rate of evolution is given by: λ = K a / 2t Poisson correction (PC) model D = 0.56 K a = -ln (1 - 0.56 ) =
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mg640Seqs - PROTEIN SEQUENCE COMPARISONS SEQUENCE...

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