DNA sequencing and restoring malformed sequences

In summary, DNA sequencing involves modeling DNA into an ordered sequence of nucleobases, with the first half representing the first strand. A random sequence can be represented as (0 1 2 0 1 1 0 3 ...) with the length being on the order of billions. If the sequence is malformed, it can be easily restored by visualizing it parallel to a correct sequence. In the context of genome sequencing, there are computationally hard problems that need to be addressed, such as assembling a full DNA sequence from multiple overlapping short fragments.
  • #1
Atran
93
1
I was just reading about DNA sequencing. In my view, DNA can be modeled into an ordered sequence of nucleobases, as if the two strands were joined into a single strand (just like in RNA). The first half of the sequence models the first strand. The four nucleobases are numbered from 0 to 3. Hence, a random sequence S equals (0 1 2 0 1 1 0 3 ...). The length of the sequence is on the order of billions.

Assume the same sequence is malformed (0 0 2 0 1 1 3 3 ...). It's malformed at position 1 and 6. Visualizing the two sequences parallel to each other, restoring the malformed sequence would be an easy computational task.

Am I missing something? I looked through this because I heard of sequencing in the context of NP-completeness in my computational complexity class.
 
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  • #2
I don't think recognizing mutations is a computationally hard problem (provided the mutation rate is sufficiently low). In the context of genome sequencing, here's a good source that describes one computationally hard problem that had to be addressed in the genome sequencing field (figuring out how to assemble a full DNA sequence from multiple overlapping short fragments of that DNA sequence): http://www.cs.cmu.edu/afs/cs/academic/class/15210-s15/www/lectures/genome-notes.pdf
 

What is DNA sequencing?

DNA sequencing is the process of determining the precise order of nucleotides (A, T, C, and G) within a DNA molecule. This information is important for understanding genetic variations and mutations, as well as for identifying genetic diseases.

Why is DNA sequencing important?

DNA sequencing allows us to understand the genetic makeup of an organism, which can provide insights into its physical characteristics, behaviors, and susceptibility to diseases. It also helps researchers develop new treatments and therapies for genetic disorders.

How is DNA sequencing done?

The most common method of DNA sequencing is called Sanger sequencing, which involves breaking down the DNA into smaller fragments, labeling them with fluorescent tags, and then using a machine to read the sequence of nucleotides. Newer methods, such as next-generation sequencing, use advanced technologies to sequence DNA faster and more accurately.

What is a malformed DNA sequence?

A malformed DNA sequence is a sequence that contains errors or mutations, such as missing or extra nucleotides, or incorrect ordering of nucleotides. These errors can occur naturally or as a result of environmental factors and can lead to genetic disorders.

How can malformed DNA sequences be restored?

There are various methods for restoring malformed DNA sequences, depending on the type and severity of the mutation. One approach is to use gene editing technologies, such as CRISPR-Cas9, to correct the error in the DNA sequence. Another method is to use gene therapy, which involves introducing a functional copy of the mutated gene to replace the faulty one.

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