In "[Genomics: A Very Short Introduction]" by John Archibald, the author discusses the DNA sequencing:

In living cells, DNA rarely exists in isolation; it is typically bound tightly to proteins (see Figure 2), proteins that serve to compact it and to regulate the process of gene expression. Consequently, the act of purifying (or ‘extracting’) DNA from the multitude of proteins, lipids, and other macromolecules inside the cell requires the use of harsh chemicals and subjects it to physical damage. While it is possible to estimate the size of intact chromosomes in the lab, modern DNA sequencing instruments typically collect at most 1,000 base pairs of nucleotide sequence per DNA fragment.

What does this sentence mean?


1 Answer 1


They are referring to sequencing strategies where you chop a longer stretch of DNA into fragments, sequence each of these, and stitch the sequences back together.

The sentence is explaining that the lengths of DNA actually sequenced from these fragments are relatively short, up to 1000 base pairs per fragment.

  • 1
    $\begingroup$ Are you sure? If this the case why don’t they just say so without reference to the sequencing machines. Without knowing any more about it, I would interpret the sentence to mean that regardless of the fragment length, the machines become inaccurate after 1000 nt. $\endgroup$
    – David
    Aug 20, 2022 at 20:01
  • $\begingroup$ I agree with David. Depending on the method of fragmentation (restriction enzyme, sonication/shearing, etc.) you can sometimes end up with fragments that are a lot longer (or a lot shorter) than 1000bp. I think the sentence is talking about the maximum usable length of a read, not the fragment size itself. $\endgroup$
    – MattDMo
    Aug 21, 2022 at 12:53
  • $\begingroup$ @MattDMo Updated to clarify that this is the sequenced length from a fragment, not the size of the fragment itself. $\endgroup$
    – Bryan Krause
    Aug 21, 2022 at 13:55

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