[Biopython] make_log_odds_matrix

[George Devaniranjan]

The biopython tutorial talks about constructing a substitution
matrix....I used the following lines of code

test_dict={('Y', 'L'): 1552226.0, ('B', 'B'): 18251943.0, ('D', 'G'):
44863831.0, ('D', 'D'): 22086473.0,...........

test_dict give the frequency which different amino acids replace each other
from Bio import SubsMat
my_arm=SubsMat.SeqMat(test_dict)


my_log=SubsMat.make_log_odds_matrix(my_arm)

my_log.print_mat()

I have 2 questions:

1) Is this the correct way to do this?

2) This seems different to the way BLOSUM is generated, there is no
"normalising" , so can we really compare this generated matrix to a
BLOSUM matrix?

Thank you,
George