[Biopython] make_log_odds_matrix
George Devaniranjan
devaniranjan at gmail.com
Fri Nov 18 22:13:58 UTC 2011
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
More information about the Biopython
mailing list