What do the scores in a BLOSUM matrix mean?

Question

[mithrandir]

For example in BLOSUM62 Matrix there are negative scores for some pairs and zero for some, what does it mean by having a negative or zero score here? I suppose the more the score the more similar the amino acids are. Am I right in saying this?

BLOSUM62 Matrix here: https://upload.wikimedia.org/wikipedia/commons/5/52/BLOSUM62.gif

Answer 1

[Jean-Karim Heriche]

The values can be negative because they are logs of odd ratios. The interpretation is that the higher the score, the more likely the corresponding amino-acid substitution is. The wikipedia article on BLOSUM has a good explanation, check the section on scoring.