Amino acids conservation score

Question

[mqbx2cat]

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

[Joe]

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

[Kristoffer Vitting-Seerup]

Could you elaborate on what you mean by aligned. To orthologous or to the genome or...?

Answer 1

[mqbx2cat]

Hi kristoffer.vittingseerup, thank you for your reply. I have aligned the orthologues sequences.