In a nucleotide substitution matrix which scores are to be calculated.
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muvinika •
Pairwise alignment substitution matrix
As I need to align 2 gene sequences. Do I need to calculate PAM and BLOSUM scores.
What is the difference between amino acid substitution matrix and nucleotide substitution matrix
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Ram
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muvinika •
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muvinika •
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1) Most protein alignment programs handle the matrices internally/use a default. I think some allow you to specify if you really want to. You usually have the option to select among a few (PAM100 or PAM250 vs. BLOSUM90 or BLOSUM45 vs ...) for example.
2) One is an amino acid substitution matrix (20x20) while the other is a nucleotide substitution matrix (4x4).
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Brice Sarver
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