<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>

CC BY-SA 4.0
2022-07-07T15:48:43.560Z
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.
Community
CC BY-SA 4.0
2022-07-09T08:57:27.573Z
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
kevin
<assembly><algorithms><k-mer><homework>
DNA genome string reconstruction from k-mer
# 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 ?
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)

**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  

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## 0 answers

