What do the scores in a BLOSUM matrix mean?
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
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mithrandir •
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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.
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Jean-Karim Heriche
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