Amino acids conservation score
Hi there,
I have my protein sequences aligned and I want to identify the most conserved amino acid in a given position and its conservation score. I tried using Consurf, but this uses the provided pdb structure and calculates the conservation score of the amino acids within the structure. I tried using Mstatx, but I could not understand how to interpret the results, as you get an output text with just numbers. What software would you recommend? Thank you
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Hi kristoffer.vittingseerup, thank you for your reply. I have aligned the orthologues sequences.
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Could you elaborate on what you mean by aligned. To orthologous or to the genome or...?
What do you want? Just a score for each amino acid in the MSA? You could try the script I wrote for this thread: A: MSA scoring tools/scripts
Or you can just use a PSSM, which gives you the proportions of each amino acid/base at a given position: A: How can extract nucleotide frequency for position on aligned sequences in clusta