Answers.Body: <p>Panel (a) shows a sequence gap-free alignment. Each row corresponds to a contiguous 15 base pair sequence of DNA (e.g. row 1 could be a human sequence, row 2 could be the equivalent mouse sequence etc.). Each column corresponds to a particular position/residue (e.g. column 1 is the 1st position of the alignment etc.).</p>
  
  <p>Panel (b) shows the sequence logo. As noted in the comments, this does not correspond to the alignment in (a). Instead, here is the corresponding logo:</p>
  
  <p><a href="https://i.sstatic.net/3jR8j.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/3jR8j.png" alt="enter image description here"></a></p>
  
  <p>From this you can intuitively understand that at the 1st sequence position you have only As and Ts and their frequency corresponds to the y-axis. For the 3rd position, you have only As, so only A is represented here in the logo etc.</p>
  
  <p>The consensus sequence is the most frequent letter at each position in the alignment, i.e. <code>[AT]TAGC</code> etc. where <code>[AT]</code> means A or T since they are jointly high in frequency (5 each).</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-07-29T15:02:32.367Z
Answers.LastActivityDate: 2019-07-29T15:31:12.983Z
Answers.LastEditDate: 2019-07-29T15:31:12.983Z
Answers.UserDisplayName: Chris_Rands
Body: <p>In bioinformatics, a <a href="https://en.wikipedia.org/wiki/Sequence_logo" rel="nofollow noreferrer">sequence logo</a> is a graphical representation of the sequence conservation of nucleotides (in a strand of DNA/RNA) or amino acids (in protein sequences).</p>
  
  <p>so, What is "aligned sequences" and "consensus sequence"?</p>
  
  <p>how can I get these sequences based on following data?</p>
  
  <p><a href="https://i.sstatic.net/umTOV.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/umTOV.png" alt="enter image description here"></a></p>
  
  <p>Figure 2.5 from the book "<a href="http://people.cs.ubc.ca/~murphyk/MLbook/" rel="nofollow noreferrer">Machine Learning - A Probabilistic Perspective</a>"</p>
  
  <p>more info about this figure at <a href="https://stats.stackexchange.com/q/419575/247356">here</a></p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-07-29T12:27:45.350Z
Comments.Text: Is this homework?
Comments.UserDisplayName: benn
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-07-29T14:01:57.740Z
Comments.Text: @KamilSJaron from the book "Machine Learning - A Probabilistic Perspective"
Comments.UserDisplayName: czlsws
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-07-29T14:03:47.307Z
Comments.Text: @KamilSJaron https://stats.stackexchange.com/q/419575/247356
Comments.UserDisplayName: czlsws
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-07-29T14:58:57.967Z
Comments.Text: @KamilSJaron what does "AT" in "be made of AT" mean?
Comments.UserDisplayName: czlsws
Tags: <phylogenetics><ngs><sequence-analysis>
Title: What is "aligned sequences" and "consensus sequence" in the context of sequence logo? How to compute these?
ThreadText: # What is "aligned sequences" and "consensus sequence" in the context of sequence logo? How to compute these?
  
  (Asked by: username_0 on 2019-07-29)
  
  In bioinformatics, a [sequence logo](https://en.wikipedia.org/wiki/Sequence_logo) is a graphical representation of the sequence conservation of nucleotides (in a strand of DNA/RNA) or amino acids (in protein sequences).
  
  so, What is "aligned sequences" and "consensus sequence"?
  
  how can I get these sequences based on following data?
  
  [![enter image description here](https://i.sstatic.net/umTOV.png)](https://i.sstatic.net/umTOV.png)
  
  Figure 2.5 from the book "[Machine Learning - A Probabilistic Perspective](http://people.cs.ubc.ca/~murphyk/MLbook/)"
  
  more info about this figure at [here](https://stats.stackexchange.com/q/419575/247356)
  
  **Tags:** phylogenetics, ngs, sequence-analysis
  
  > **Comments:**
  > **username_1**: Is this homework?  
  > **username_0**: @KamilSJaron from the book "Machine Learning - A Probabilistic Perspective"  
  > **username_0**: @KamilSJaron https://stats.stackexchange.com/q/419575/247356  
  > **username_0**: @KamilSJaron what does "AT" in "be made of AT" mean?  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2019-07-29. Score: 5 | Accepted answer
  
  Panel (a) shows a sequence gap-free alignment. Each row corresponds to a contiguous 15 base pair sequence of DNA (e.g. row 1 could be a human sequence, row 2 could be the equivalent mouse sequence etc.). Each column corresponds to a particular position/residue (e.g. column 1 is the 1st position of the alignment etc.).
  
  Panel (b) shows the sequence logo. As noted in the comments, this does not correspond to the alignment in (a). Instead, here is the corresponding logo:
  
  [![enter image description here](https://i.sstatic.net/3jR8j.png)](https://i.sstatic.net/3jR8j.png)
  
  From this you can intuitively understand that at the 1st sequence position you have only As and Ts and their frequency corresponds to the y-axis. For the 3rd position, you have only As, so only A is represented here in the logo etc.
  
  The consensus sequence is the most frequent letter at each position in the alignment, i.e. `[AT]TAGC` etc. where `[AT]` means A or T since they are jointly high in frequency (5 each).
  
  
  ---
  
  