Body: <p>I would like to ask how I can interpret objectively multiple alignment results. I have used JALVIEW  and TCOFFEE.</p>
  <ol>
  <li>I would like to ask if consistency score plays any role in the interpretation?</li>
  <li>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,</li>
  <li>I am curious why there is no dot beneath some columns with almost identical amino acids (expect one sequence for example).<a href="https://i.sstatic.net/CRb7F.jpg" rel="nofollow noreferrer"><img src="https://i.sstatic.net/CRb7F.jpg" alt="enter image description here" /></a></li>
  </ol>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-04-27T11:37:06.653Z
Comments.Text: Good question but we will need to know what the purpose of conservation analysis is. Make primers? State "region of conservation"? Design a vaccine?
Comments.UserDisplayName: M__
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-04-27T18:35:15.833Z
Comments.Text: the ultimate goal is to find some information about the structure and the function of an unknown protein sequence.
Comments.UserDisplayName: marilu
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-04-27T18:48:19.573Z
Comments.Text: Thanks I'll respond in a few days, my apologies for the delay in advance.
Comments.UserDisplayName: M__
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-04-27T19:00:38.863Z
Comments.Text: no worries!thank you so much for your help!i am grateful!
Comments.UserDisplayName: marilu
Tags: <phylogenetics><proteins>
Title: How can I interpret multiple alignment results?
ThreadText: # How can I interpret multiple alignment results?
  
  (Asked by: username_0 on 2020-04-27)
  
  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](https://i.sstatic.net/CRb7F.jpg)](https://i.sstatic.net/CRb7F.jpg)
  
  **Tags:** phylogenetics, proteins
  
  > **Comments:**
  > **username_1**: Good question but we will need to know what the purpose of conservation analysis is. Make primers? State "region of conservation"? Design a vaccine?  
  > **username_0**: the ultimate goal is to find some information about the structure and the function of an unknown protein sequence.  
  > **username_1**: Thanks I'll respond in a few days, my apologies for the delay in advance.  
  > **username_0**: no worries!thank you so much for your help!i am grateful!  
  
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  ## 0 answers
  
  