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I'm looking for the probabilities of amino acid substitutions in protein sequences.
A matrix of probabilities for every combination of amino acids (something like BLOSUM or PAM matrices but more universal and with raw probability values, not scores) is sought but alternatively, any method to ascertain this will be appreciated.

[EXTRA] If all diagonal values in such a matrix would be equal to 1, or you know any way to achieve that I'd be blessed.

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  • $\begingroup$ Thats doable its been done many times. What is your application and your data? What does "data in every other type" mean? There isn't really a 'universal' matrix $\endgroup$
    – M__
    Oct 8 '20 at 16:09
  • $\begingroup$ I want to use the matrix to check the probability of amino acid substitution in sequence one by one. "Data in every other type" - I just want the probability values, it can be on a web page, in an article, no matter, I'll build the matrix myself if it'll be necessary. Ye, I know there is no 'universal' matrix but anything will be fine. I just need to know how the purpose it serves. $\endgroup$
    – maciejwww
    Oct 8 '20 at 17:12
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    $\begingroup$ You mean something like BLOSUM or PAM? The details will always depend on what species you are comparing. $\endgroup$
    – terdon
    Oct 9 '20 at 12:54
  • $\begingroup$ Ye, I know them but I'm not sure they'll be useful to me. I'm aware of this but the sequences I'm working with are not labeled and I'm looking for any universal solution. Recently, I was thinking about matrices with ones on a diagonal because it'd be easier to understand to people. $\endgroup$
    – maciejwww
    Oct 10 '20 at 13:54
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The LG model is here:

0.425093 
0.276818 0.751878 
0.395144 0.123954 5.076149 
2.489084 0.534551 0.528768 0.062556 
0.969894 2.807908 1.695752 0.523386 0.084808 
1.038545 0.363970 0.541712 5.243870 0.003499 4.128591 
2.066040 0.390192 1.437645 0.844926 0.569265 0.267959 0.348847 
0.358858 2.426601 4.509238 0.927114 0.640543 4.813505 0.423881 0.311484 
0.149830 0.126991 0.191503 0.010690 0.320627 0.072854 0.044265 0.008705 0.108882 
0.395337 0.301848 0.068427 0.015076 0.594007 0.582457 0.069673 0.044261 0.366317 4.145067 
0.536518 6.326067 2.145078 0.282959 0.013266 3.234294 1.807177 0.296636 0.697264 0.159069 0.137500 
1.124035 0.484133 0.371004 0.025548 0.893680 1.672569 0.173735 0.139538 0.442472 4.273607 6.312358 0.656604 
0.253701 0.052722 0.089525 0.017416 1.105251 0.035855 0.018811 0.089586 0.682139 1.112727 2.592692 0.023918 1.798853 
1.177651 0.332533 0.161787 0.394456 0.075382 0.624294 0.419409 0.196961 0.508851 0.078281 0.249060 0.390322 0.099849 0.094464 
4.727182 0.858151 4.008358 1.240275 2.784478 1.223828 0.611973 1.739990 0.990012 0.064105 0.182287 0.748683 0.346960 0.361819 1.338132 
2.139501 0.578987 2.000679 0.425860 1.143480 1.080136 0.604545 0.129836 0.584262 1.033739 0.302936 1.136863 2.020366 0.165001 0.571468 6.472279 
0.180717 0.593607 0.045376 0.029890 0.670128 0.236199 0.077852 0.268491 0.597054 0.111660 0.619632 0.049906 0.696175 2.457121 0.095131 0.248862 0.140825 
0.218959 0.314440 0.612025 0.135107 1.165532 0.257336 0.120037 0.054679 5.306834 0.232523 0.299648 0.131932 0.481306 7.803902 0.089613 0.400547 0.245841 3.151815 
2.547870 0.170887 0.083688 0.037967 1.959291 0.210332 0.245034 0.076701 0.119013 10.649107 1.702745 0.185202 1.898718 0.654683 0.296501 0.098369 2.188158 0.189510 0.249313 

Where the amino acid frequencies are:

0.079066 0.055941 0.041977 0.053052 0.012937 0.040767 0.071586 0.057337 0.022355 0.062157 0.099081 0.064600 0.022951 0.042302 0.044040 0.061197 0.053287 0.012066 0.034155 0.069147

Amino acid order (matrix and frequencies)

A R N D C Q E G H I L K M F P S T W Y V

Reference Le S.Q., Gascuel O. Molecular Biology and Evolution. 2008 25(7):1307-20.

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