Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Tutorials
Tools
Jobs
Forum
Planet
All »
Home
Log In
Question: Pairwise alignment substitution matrix
0
gravatar for muvinika
5.7 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 • 2.3k views
ADD COMMENT • link •
modified 5.7 years ago by Brice Sarver • 3.6k • written 5.7 years ago by muvinika • 0
0
gravatar for Brice Sarver
5.7 years ago by
Brice Sarver • 3.6k
United States
Brice Sarver • 3.6k 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 5.7 years ago by Brice Sarver • 3.6k

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

ADD REPLY • link written 5.7 years ago by muvinika • 0
Please log in to add an answer.

Similar posts • Search »

Content
Help
Access
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2254 users visited in the last hour
_