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Question: Pairwise alignment substitution matrix
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gravatar for muvinika
4.0 years ago by
muvinika • 0
muvinika • 0 wrote:

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
sequencing sequence alignment gene • 1.8k views
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modified 4.0 years ago by Brice Sarver • 2.6k • written 4.0 years ago by muvinika • 0
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gravatar for Brice Sarver
4.0 years ago by
Brice Sarver • 2.6k
United States
Brice Sarver • 2.6k wrote:

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).
ADD COMMENT • link written 4.0 years ago by Brice Sarver • 2.6k

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

ADD REPLY • link written 4.0 years ago by muvinika • 0
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