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In the blosum-62 substitution matrix, a large positive score corresponds to substitution that occurs frequently.
BLOSUM-62 is used to account for the type of substitution when comparing sequences. To identify the problem the first approach is examining the substitutions that have actually taken place in evolutionary related proteins.
From an examination of appropriately aligned sequences, substitution matrices have been deduced. A substitution matrix describes a scoring system for the replacement of any amino acid with each of the other 19 amino acids.
In these matrices, a large positive score corresponds to a substitution that only occurs relatively frequently, whereas a large negative score corresponds to a substitution that only occurs rarely. A commonly used matrix, the BLOSUM-62 stands for Blocks of amino acid substitution matrix.
Each column in the matrix represents one of the 20 amino acids, whereas the position of the single letter codes within each column specify the score for the corresponding substitution.
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