Pairwise alignment substitution matrix

Question

[muvinika]

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

Answer 1

[Brice Sarver]

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).

[muvinika]

In a nucleotide substitution matrix which scores are to be calculated.