Body: <p>I'm investigating two different groups of short nucleotide sequences. The behaviour of a certain DNA-binding protein is likely influenced by common differences between these two groups leading high or low activity. Some positions are hypothesized to be more important than others. All sequences have the same length and are very similar.</p>
  <p>I'm trying to find out how well changes at certain sequence positions explain the between-group difference and which positions are of the highest importance for this relationship. By looking at the sequence logo for both groups I can easily identify crucial positions. However, I'm at a loss how to actually score the effect each position has and how well it correlates to membership in either group. I thought about calculating Cramers V at each position but that doesn't seem to be very useful.</p>
  <p>Can someone here point me in the right direction?</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-05-31T13:38:47.137Z
Comments.Text: Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.
Comments.UserDisplayName: Community
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-05-31T18:08:13.493Z
Comments.Text: are you talking about a _sequence alignment_ of homologous sequences? Can you include a sample of what your data look like? Recall that [the logo is based on sequence entropy](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC419797/), why not use that measurement?
Comments.UserDisplayName: Maximilian Press
Tags: <r><phylogenetics>
Title: Calculating the effect of differences between two groups of nucleotide sequences at every position
ThreadText: # Calculating the effect of differences between two groups of nucleotide sequences at every position
  
  (Asked by: username_0 on 2022-05-31)
  
  I'm investigating two different groups of short nucleotide sequences. The behaviour of a certain DNA-binding protein is likely influenced by common differences between these two groups leading high or low activity. Some positions are hypothesized to be more important than others. All sequences have the same length and are very similar.
  
  I'm trying to find out how well changes at certain sequence positions explain the between-group difference and which positions are of the highest importance for this relationship. By looking at the sequence logo for both groups I can easily identify crucial positions. However, I'm at a loss how to actually score the effect each position has and how well it correlates to membership in either group. I thought about calculating Cramers V at each position but that doesn't seem to be very useful.
  
  Can someone here point me in the right direction?
  
  **Tags:** r, phylogenetics
  
  > **Comments:**
  > **username_1**: Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.  
  > **username_2**: are you talking about a _sequence alignment_ of homologous sequences? Can you include a sample of what your data look like? Recall that [the logo is based on sequence entropy](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC419797/), why not use that measurement?  
  
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  ## 0 answers
  
  