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Old 09-27-2011, 04:08 AM   #1
pmaugeri
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Default The meaning of "realtime" here

Hi

I read the product description of the instrument:

"The PacBio RS system conducts, monitors and analyzes single molecule, realtime (SMRT™) sequencing reactions.
[...]
These signals are delivered in real time to the primary analysis pipeline, housed entirely on the Blade Center."

Could you please explain to me the meaning of "realtime" here? What is the purpose of getting notified in realtime of the signals?

Thanks in advance
Pascal
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Old 09-27-2011, 04:21 AM   #2
GenoMax
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The "real-time" is referring to how the detection works in a PacBio sequencer.

One is observing (figuratively speaking) a single polymerase molecule replicate DNA in each zero-mode wave guide (ZMV) using split beams from a laser (75,000 ZMV's at one time .. how cool is that!). The polymerase is modified to slow its processing speed down to a couple of nucleotides (per second) so the lasers can keep up with the detection. The resulting "movie" is then analyzed on the primary cluster included in the instrument before the results are written to external storage (that you provide).

Videos for technology: http://www.pacificbiosciences.com/ab...pac_bio_lg.jpg

Quote:
Originally Posted by pmaugeri View Post
Hi

Could you please explain to me the meaning of "realtime" here? What is the purpose of getting notified in realtime of the signals?

Thanks in advance
Pascal

Last edited by GenoMax; 09-27-2011 at 04:48 AM.
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Old 10-24-2011, 02:07 PM   #3
rskr
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A good counter example would be GAIIX which iteratively takes essentially static images of a bunch of cells, and then at some point and time later they are analyzed. The HiSeq would be somewhere in between, not exactly real-time, but do to the high volume they don't store the entire thing either, but they can.

It seems that a pacbio machine has the potential to do more types of analysis than simple sequencing such as detecting dna modifications including but not limited to methylation. The draw back appears that the analysis needs to be conducted in real-time, due to the very large amount of data that is generated in the most basic detection, isn't possible to be stored.

The way I see it real-time isn't necessarily a good thing, because it makes it more difficult to develop an analysis, and I am not aware of any official pacbio packages for these potential applications.
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