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Unformatted text preview: BIOC3608 – Introduction to Bioinformatics 2008 BLOSUM 1. Count the number of matches and mismatches of each type (f ij ) 2. Calculate the observed probably of occurrence (q ij ) for each amino acids pair i ,j 3. Calculate the probability of occurrence of amino acids 4. Calculate expected probability of occurrence for each amino acids pair i, j (e ij ) 5. Calculate S ij = 2 x log 2 (q ij /e ij ) PAM 1. Align sequences that are at least 85% identical 2. Reconstruct a phylogenetic tree and infer ancestral sequences (sequences 1- 5 ) such that minimum number of mutations are required 3. Count the number of mutations between ancestral sequences and database sequences. Substitutions are counted in both directions, i.e. K Q is also counted as Q K 4. Construct a mutation (substitution) probability matrix 1. 2. (a) Local alignment method. Because they share a common domain and have high degree of similarity. 2. (b) Smith-Waterman local alignment method. Because its useful in identifying alignment in subsequence....
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- Summer '09
- Limit of a sequence, Sequence alignment, Computational phylogenetics