Body: <p>I have the following quiz question, but the Pattern1 for both <code>(ACC|ATA)</code> and <code>(CGA|ACT)</code> are unique (just grep for <code>ACC</code> and <code>CGA</code>), which means it might be difficult to find the starting pattern for the DNA genome string in the following case. Do I need something like <a href="https://sci-hub.ee/https://ieeexplore.ieee.org/document/8247239" rel="nofollow noreferrer">GapReduce algorithm</a> ?</p>
  <p>Quiz : There is a single (linear) string with the following (3,1)-mer composition. Find it.</p>
  <pre><code>(ACC|ATA) (ACT|ATT) (ATA|TGA) (ATT|TGA) (CAC|GAT) (CCG|TAC) (CGA|ACT)
  
  (CTG|AGC) (CTG|TTC) (GAA|CTT) (GAT|CTG) (GAT|CTG) (TAC|GAT) (TCT|AAG)
  
  (TGA|GCT) (TGA|TCT) (TTC|GAA)
  </code></pre>
  <p><a href="https://i.sstatic.net/QT9yQ.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/QT9yQ.png" alt="k-d mer" /></a></p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-07-07T15:48:43.560Z
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: 2022-07-09T08:57:27.573Z
Comments.Text: As shown in the picture in the question, just align the (k, d)-mers vertically without the help of assembler software, then compare whether they conflict with each other vertically. Maybe the software to do such comparison uses https://en.wikipedia.org/wiki/Smith%E2%80%93Waterman_algorithm
Comments.UserDisplayName: kevin
Tags: <assembly><algorithms><k-mer><homework>
Title: DNA genome string reconstruction from k-mer
ThreadText: # DNA genome string reconstruction from k-mer
  
  (Asked by: username_0 on 2022-07-07)
  
  I have the following quiz question, but the Pattern1 for both `(ACC|ATA)` and `(CGA|ACT)` are unique (just grep for `ACC` and `CGA`), which means it might be difficult to find the starting pattern for the DNA genome string in the following case. Do I need something like [GapReduce algorithm](https://sci-hub.ee/https://ieeexplore.ieee.org/document/8247239) ?
  
  Quiz : There is a single (linear) string with the following (3,1)-mer composition. Find it.
  
  ```
  (ACC|ATA) (ACT|ATT) (ATA|TGA) (ATT|TGA) (CAC|GAT) (CCG|TAC) (CGA|ACT)
  
  (CTG|AGC) (CTG|TTC) (GAA|CTT) (GAT|CTG) (GAT|CTG) (TAC|GAT) (TCT|AAG)
  
  (TGA|GCT) (TGA|TCT) (TTC|GAA)
  
  ```
  
  [![k-d mer](https://i.sstatic.net/QT9yQ.png)](https://i.sstatic.net/QT9yQ.png)
  
  **Tags:** assembly, algorithms, k-mer, homework
  
  > **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_0**: As shown in the picture in the question, just align the (k, d)-mers vertically without the help of assembler software, then compare whether they conflict with each other vertically. Maybe the software to do such comparison uses https://en.wikipedia.org/wiki/Smith%E2%80%93Waterman_algorithm  
  
  ---
  
  ## 0 answers
  
  