Question: Amino acid Changes Substitution score
0
gravatar for muvinika
4.7 years ago by
muvinika0
muvinika0 wrote:

Hi,

How do we calculate Amino acid Changes Substitution score for mutations in the gene sequences? Could you please explain about the calculation of grantham score?

sequence gene genome • 4.2k views
ADD COMMENTlink modified 4.7 years ago by Ashutosh Pandey11k • written 4.7 years ago by muvinika0
1
gravatar for Ashutosh Pandey
4.7 years ago by
Philadelphia
Ashutosh Pandey11k wrote:

Here is the link to the paper http://www.sciencemag.org/content/185/4154/862.long

AMINO ACID DIFFERENCE FORMULA TO HELP EXPLAIN PROTEIN EVOLUTION

A formula for difference between amino acids combines properties that correlate best with protein residue substitution frequencies: composition, polarity, and molecular volume. Substitution frequencies agree much better with overall chemical difference between exchanging residues than with minimum base changes between their codons. Correlation coefficients show that fixation of mutations between dissimilar amino acids is generally rare.

In case you are looking for the code, you can modify this python code and use it:

https://github.com/ashutoshkpandey/Annotation/blob/master/Grantham_score_calculator.py

ADD COMMENTlink modified 4.7 years ago • written 4.7 years ago by Ashutosh Pandey11k
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