Albert-Ludwigs-Universität Freiburg
Lehrstuhl für Bioinformatik - Institut für Informatik - http://www.bioinf.uni-freiburg.de
After manually calculating the PAM matrices in the exercise 1, you are now tasked to implement each of the steps. Make use of the formulae introduced before. All of the functions should take an argument called sym_align which represents the symmetric algignment as a tuple of strings
a) Implement the calculation of the nucleotide frequencies for a symmetric alignment. Make sure that the indexing works the following way:
- [0] = A
- [1] = C
- [2] = T
- [3] = G
b) Implement the calculation of the mutation matrix. Remember indexing as in the previous exercise.
c) Implement the calculation of the unnormalized PAM scores. Remember indexing as in the previous exercise.
d) Implement the calculation of the normalization factor gamma.
e) Implement the calculation of the probability matrix.
f) Implement the calculation of the normalized probability matrix.
g) Implement the calculation of the PAM matrix. Make sure to round values to integers.