Question: Pairwise alignment substitution matrix
0
gravatar for muvinika
4.4 years ago by
muvinika0
muvinika0 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

ADD COMMENTlink modified 4.4 years ago by Brice Sarver3.2k • written 4.4 years ago by muvinika0
0
gravatar for Brice Sarver
4.4 years ago by
Brice Sarver3.2k
United States
Brice Sarver3.2k 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 COMMENTlink written 4.4 years ago by Brice Sarver3.2k

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

ADD REPLYlink written 4.4 years ago by muvinika0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2001 users visited in the last hour