BLOSUM scores compared to PAM scores

Question

[Mathis]

Hello

Anybody who might be able to help me understand why the scores in general is smaller in the BLOSUM matrix compared to the PAM matrix?

Thanks

Best regards

Answer 1

[Ram]

They are fundamentally different measures. One measures the degree of conservation among related proteins and one measures the amount of change seen in sequences that have a certain percent of tolerated mutations. Directly comparing their absolute numbers will not make sense, because they are relative measures, which means you'll be comparing PAM scored for various alignments or BLOSUM scores for various alignments, but not PAM score for an AA change vs the BLOSUM score for the same change.

Answer 2

[natasha.sernova]

See these links:

http://www.majordifferences.com/2014/02/difference-between-pam-and-blosum-matrix_1.html

http://www.cs.columbia.edu/4761/assignments/assignment1/reference1.pdf

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3848038/

F nice conclusion about all kinds of matrices:

http://bip.weizmann.ac.il/education/course/introbioinfo/lect5/scoringmatrices07.pdf