University:
The University Of Western Ontario
Course:
2483A | Ecology
Academic year:

2024
Views:

374

Pages:

2
Author:

Kyuwon J.

Substitution Matrix Requirement 1. Must be able to give score>0 2. Should give scores <=0 for random sequences Empirical Solution ● Estimate scores based on observed frequencies from sequence alignments Real Substitution Matrix Expected Value: The expected value per AA pair between random sequences Here, it is -0.5206 Entropy: The amount of information on average from a AA pair. Here it is 0.6979 ● High entropy=mismatches penalized more ● Low entropy=permits more distant alignments ● BLOSUM/PAM with similar entropy~equivalent Calculating Scoring Matrix 𝑆𝑐𝑜𝑟𝑒(𝑎 → 𝑏) = λ𝑙𝑜𝑔 𝑃(𝑎→𝑏) 𝑃(𝑎)*𝑃(𝑏) Numerator=> observed Denominator=> Expected ex) Lets take an example:Proline -> Glycine 𝑃(𝑎 → 𝑏) = probability Proline is substituted by glycine 𝑃(𝑎) = Probability a randomly selected amino acid is Proline 𝑃(𝑏) = Probability a randomly selected amino acid is Glycine These are calculated form the same source

Substitutiution Matrix

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