Comments on: Helicos Biosciences is reporting the sequencing of M13 in Science. http://synthesis.williamgunn.org/2008/04/08/helicos-biosciences-is-reporting-the-sequencing-of-m13-in-science/ A synthesis of ideas about open science and social technology. Wed, 18 Jan 2012 20:57:43 +0000 hourly 1 http://wordpress.org/?v=3.3.1 By: Mr. Gunn http://synthesis.williamgunn.org/2008/04/08/helicos-biosciences-is-reporting-the-sequencing-of-m13-in-science/comment-page-1/#comment-7640 Mr. Gunn Wed, 09 Apr 2008 21:30:08 +0000 http://synthesis.williamgunn.org/?p=186#comment-7640 Thanks for your comments, Eric. In practice, longer reads than 17 are needed, and Helicos is getting around 23, which gets them close to where they need to be. I was simply showing the reasoning behind the number. I don't have any insider information that Helicos is actually using FRET, but from reading what's been published leading up to this, that's certainly what it sounds like. It's also consistent with the exorbitant instrument prices they're listing. Thanks for your additional link, too. I meant to include it in the original post and lost it somehow in the plethora of tabs I had open. Thanks for your comments, Eric. In practice, longer reads than 17 are needed, and Helicos is getting around 23, which gets them close to where they need to be. I was simply showing the reasoning behind the number.

I don’t have any insider information that Helicos is actually using FRET, but from reading what’s been published leading up to this, that’s certainly what it sounds like. It’s also consistent with the exorbitant instrument prices they’re listing.

Thanks for your additional link, too. I meant to include it in the original post and lost it somehow in the plethora of tabs I had open.

]]> By: Eric http://synthesis.williamgunn.org/2008/04/08/helicos-biosciences-is-reporting-the-sequencing-of-m13-in-science/comment-page-1/#comment-7416 Eric Wed, 09 Apr 2008 02:38:04 +0000 http://synthesis.williamgunn.org/?p=186#comment-7416 Thanks for the link Mr. Gunn! :D Couple comments on your post... I'm not sure what the latest experiences are on read length needed for efficient de novo human sequencing, but it's much much longer than 17 for humans, considering the number of repeats and similar regions. I might be getting my providers/technologies mixed up, but AFAIK there has not been confirmation publicly that Helicos uses FRET. There was some initial discussion of it between a labeled template strand and the incorporated nucleotide (http://biotechnicalcurrency.blogspot.com/2007/07/helicos-part-ii_25.html), but no confirmation on helicosbio.com...I'm interested in this, as this type of FRET will limit their read length (versus say a Visigen polymerase-nuc FRET setup). Last but not least, Illumina consumables are ~$2-3k per sample (so ~$25k for an 8 sample run.) There is further (humorous?) discussion of this paper here on my site: http://seqanswers.com/forums/showthread.php?t=191 Thanks for the link Mr. Gunn! :D

Couple comments on your post…

I’m not sure what the latest experiences are on read length needed for efficient de novo human sequencing, but it’s much much longer than 17 for humans, considering the number of repeats and similar regions.

I might be getting my providers/technologies mixed up, but AFAIK there has not been confirmation publicly that Helicos uses FRET. There was some initial discussion of it between a labeled template strand and the incorporated nucleotide (http://biotechnicalcurrency.blogspot.com/2007/07/helicos-part-ii_25.html), but no confirmation on helicosbio.com…I’m interested in this, as this type of FRET will limit their read length (versus say a Visigen polymerase-nuc FRET setup).

Last but not least, Illumina consumables are ~$2-3k per sample (so ~$25k for an 8 sample run.)

There is further (humorous?) discussion of this paper here on my site: http://seqanswers.com/forums/showthread.php?t=191

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