My first university biology classes begin in September. In preparation, but increasingly out of curiosity, I've been studying some basic biology. Saying that to say, I know as much about DNA replication as the Khan Academy videos teach.

Presently, I'm reading about the two efforts to sequence the genome. From what I've read, Collins' project used "polymerase catalysis and nucleotide labeling"; whereas, Venter's project used "shotgun sequencing". I didn't know enough to understand the article I read on "shotgun sequencing" and couldn't find one that described the other technique.

I suspect that, in order to comprehend a concise description of the two techniques, I'd need to learn more than I could learn from an answer to this question. That said, it'd still be nice to have a very rough idea of what each process involves and how they differ from each other. A crude analogy to something concrete would be great.

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    $\begingroup$ You should read about chain-termination (aka Sanger) sequencing; it was used by both projects. Shotgunning is a technique used to assemble an entire genome out of the many short reads from the sequencer. The private project used whole genome shotgunning whereas the public project used the clone contig approach. This looks like a good read for you: ncbi.nlm.nih.gov/books/NBK21117/#!po=29.2373 $\endgroup$ – canadianer Aug 5 '15 at 1:31

The public effort, led by Collins, relied on a physical map of each chromosome. Very large pieces of genomic DNA were sub cloned into cloning vectors and used to create genomic libraries in cosmids, BACs and YACs. The sub clones are ordered using hybridization probes from either known genes, or RFLP genetic markers. In this way a physical map of each chromosome was built up, and then the project would march down the ordered clones, sequencing the sub clones. If the physical map is good then you have a very good idea of where the sequence comes from.

Shotgun sequencing, in contrast, involves randomly fragmenting the entire genome into small fragments (using sonication, for example), sub cloning those pieces and sequencing everything.

In the first method each base is sequenced a minimal number of times, whereas in the second approach each base ends up being sequenced many times (on average).

For a whole genome, shotgun sequencing requires an excellent computer algorithm to "assemble" the resulting data into overlapping contigs.

  • $\begingroup$ What information informs the 'decisions' of the algorithm, and what sort of decisions is it making? $\endgroup$ – Hal Aug 5 '15 at 1:03
  • $\begingroup$ Good answer, though I'm not sure how useful it will be for someone just starting biology ;) $\endgroup$ – canadianer Aug 5 '15 at 1:24
  • $\begingroup$ I don't think I have the expertise to compare and contrast the pros and cons of the competing approaches. Have you read the Wikipedia entry on the Human Genome Sequence? There are many good references there. If you are interested in Venter & Gene Myers' algorithm you may find Michael Ashburner's short book about sequencing the Drosophila genome helpful. That was essentially a dry run for the Human effort, and they developed the tools then. Matt Ridley's book "Genome" has a good description of the shotgun approach, as I recall. $\endgroup$ – RosieF Aug 5 '15 at 1:29

PCR (polymeraze chain reaction) and shotgun sequencing are two somewhat complimentary approaches to sequencing. In the former case one uses chemical reaction to create multiple copies of the genome of interest, which allows to reduce the error in sequencing this genome. The latter is done by sequencing the data directly, i.e., without any genome multiplication.

PCR is more suitable when we are studying a particular genome or a few genomes, e.g., when sequencing the genome of a particular person or a particular type of organism. However, when some very different genomes are present, the amplification might be very uneven, and in fact introduce additional errors. This is why in some situations one prefers shotgun sequencing, e.g., when studying microbiome, containing many different types of bacteria, archaea, viruses, etc.

Both terms refer to the so-called High-Throughput Sequencing (HTS). You could learn a bit more about sequencing technologies from this popular science article.


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