Question: What do the scores in a BLOSUM matrix mean?
gravatar for mithrandir
3.2 years ago by
mithrandir40 wrote:

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

ADD COMMENTlink modified 3.2 years ago by Jean-Karim Heriche18k • written 3.2 years ago by mithrandir40
gravatar for Jean-Karim Heriche
3.2 years ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche18k wrote:

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.

ADD COMMENTlink written 3.2 years ago by Jean-Karim Heriche18k
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