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I would like to ask how I can interpret objectively multiple alignment results. I have used JALVIEW and TCOFFEE.

  1. I would like to ask if consistency score plays any role in the interpretation?
  2. I would like to ask for a region of a protein to be considered conserved, all the amino acids should have similar properties? So even if only one protein has a different amino acid (among the proteins that are included in the multiple alignment), then there is no conservation? for example, in this picture,
  3. I am curious why there is no dot beneath some columns with almost identical amino acids (expect one sequence for example).enter image description here
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  • $\begingroup$ Good question but we will need to know what the purpose of conservation analysis is. Make primers? State "region of conservation"? Design a vaccine? $\endgroup$ – Michael Apr 27 at 11:37
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    $\begingroup$ the ultimate goal is to find some information about the structure and the function of an unknown protein sequence. $\endgroup$ – marilu Apr 27 at 18:35
  • $\begingroup$ Thanks I'll respond in a few days, my apologies for the delay in advance. $\endgroup$ – Michael Apr 27 at 18:48
  • $\begingroup$ no worries!thank you so much for your help!i am grateful! $\endgroup$ – marilu Apr 27 at 19:00

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