MATLAB aminolookup converting reference

Hello guys. I am using Bioinformatic Toolbox of MATLAB.

In order to convert protein sequences to the integer representations, MATLAB provides us to apply aminolookup function.

Yet when i see the table, it has different values for differen amino acid codes. In MATLAB A is 1, R is 2, N is 3, and so on. However in the literature A is 1, C is 2, D is 3 and so on. Why is the difference? Is there any reference for it?

Answer 1

[Tim DeFreitas]

There is no inherent meaning to the values assigned to each amino acid, they are arbitrary. In general, they are in alphabetical order by full Amino Acid name, with the ambiguous codes at the end (e.g. B/Z/X/*). More details can be found here:

https://www.mathworks.com/help/bioinfo/ref/aa2int.html#bq61iz1-1