Question: Amino acids conservation score
gravatar for mqbx2cat
11 days ago by
mqbx2cat0 wrote:

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

sequence alignment • 234 views
ADD COMMENTlink modified 9 days ago • written 11 days ago by mqbx2cat0

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

ADD REPLYlink written 9 days ago by jrj.healey2.0k

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

ADD REPLYlink written 11 days ago by kristoffer.vittingseerup210
gravatar for mqbx2cat
9 days ago by
mqbx2cat0 wrote:

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

ADD COMMENTlink written 9 days ago by mqbx2cat0
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