James and the Giant Corn Genetics: Studying the Source Code of Nature

February 25, 2010

Ion Torrent Sequencing

Filed under: genomics — Tags: , — James @ 12:31 am

I know absolutely nothing about their technology (they’ve been playing things much closer to their chests than Pacific Biosystems), but they just announced they’d start delivering their machines by the end of this year and that they’ll reveal the principles of their new technology in a talk on Saturday.

Marco Island, Florida (where the Advances in Genome Biology and Technology conference is being held) is certainly the place to be this week.

Greg Baute’s optimistic predictions about the year 2010 in sequencing may prove more accurate than my own pessimism yet.

February 24, 2010

Map of the Places That Get the First PacBio Sequencers

Filed under: genomics — Tags: , — James @ 1:13 am

In all honesty, I don’t know how big a difference Pacific Biosystem’s technology* will make to genomics. I doubt anyone can until the machines are actually in use by sequencing centers and people can start to make judgements about how they behave under real life conditions. How much sequence can actually be produced per day or per dollar? How long will the reads actually get? What sort of sequencing errors are most common with the technology and how common are they?

But now I know the people who will be the first to find out the answers to these questions. Today (yesterday by the time this is scheduled to publish) Pacific Biosystem’s announced where the first ten of their new sequencing machines will be going:

View Pacific Biosystems Sequencers in a larger map (click the markers to see the names of the institutions receiving the sequencers)


January 29, 2010

New SOLiD Sequencers, and the ever dropping cost of sequencing

Filed under: Uncategorized — Tags: , , — James @ 8:20 pm

David Dooling, writing at PolITgenomics, brings word of the announcement of a new generation of SOLiD sequencing machines. The statistics aren’t quite as impressive as the Illumina HiSeq 2000 announced a couple of weeks ago, but it will be cheaper per gigabase of sequence.

As long as SOLiD sequencing can keep giving Illumina a run for its money, the price of sequencing is going to keep dropping, and the R&D departments of both companies will be working round the clock to keep the improvements coming (SOLiD is already promising upgrades that will triple the amount of sequence generated per run, while cutting the cost of each run by half (6x reduction in cost/GB of sequence)… by the end of this year.) (more…)

January 13, 2010

Even Faster Sequencing

Filed under: Fun With Numbers — Tags: , , , — James @ 12:01 pm

Just five years ago in 2005, the state of the art technology for sequencing genomes was Sanger sequencing, the same basic technology that had been used by biologists for decades, although the sequencers of 2005 were the result of decades of refinement of the basic technique. Five years later in 2010, the newest state of the art sequencer is the HiSeq 2000 from Illumina (at least until the Pacific Biosystems sequencers become available later this year… ::drool::). What difference does 5 years make? It would take more than thirty-thousand of the latest and greatest sanger sequencers from 2005 (right before the first next generation sequencer, a 454 machine built by Roche, was released) to produce as much DNA sequence data as a single one of the new HiSeq 2000s produces.* (more…)

November 26, 2009

The Cost of the Turkey Genome

Filed under: Genetics,Link Posts — Tags: , , — James @ 6:52 pm

Just to give you a sense of how fast technology is advancing:

Sequencing the maize genome took four years and 30 million dollars. Today Virginia Tech announced the University of Minnesota and themselves had received a $908,000 grant to sequence the Turkey genome in two years. I don’t know how big or complex the turkey genome is, but the idea of sequencing a whole new species for less than a million dollars is still pretty cool.

h/t to 538 they’ve got more cool turkey statistics over there.

November 23, 2009

The Domestication of Maize

Twenty thousand years ago, not a single crop species existed in its current form. Almost* every bite of food you eat today is the result huge amounts of human artificial selection, both unconsciously and intentionally by farmers and plant breeders. Sometimes the obvious changes are minor, for example between wild and domesticated strawberries:

Wild strawberry (left) and domesticated strawberry (right)

Wild strawberry (left) and domesticated strawberry (right)

Clearly one of the major traits early strawberry growers selected for was bigger fruits. Which makes sense since it takes about the same amount of time an effort to pick a strawberry either way, but if you’re picking the ones on the right you’ll have more pounds of fruit picked at the end of the day.

But even in this case, the similarity in form hides major changes at the genome left. Strawberries went through two whole genome duplications during domestication (looks like it’s more complicated than I made it sound see comments), so each of the cells in the strawberries on the right contain eight copies of each chromosome, while the strawberry on the left contains the more standard two copies of each chromosome.

On the other end of the spectrum is maize. (more…)

November 20, 2009

Patrick Schnable on the Maize Genome

Filed under: Genetics,Plants — Tags: , , , , — James @ 1:25 am

Let me know if you have any trouble with the embedded video. The embedding code from ISU doesn’t seem to play well with wordpress.

I’ve got several posts on the maize genome coming out scheduled to go up later today. Living on the west coast (not to mention having a circadian clock that seems convinced I should actually be living on Honolulu time) it’s the only way to get information up in time for morning readers in most of the US.

Anyway, hopefully some of what I’ve written makes sense (I’ll be running a lot of long computational jobs at work so I’ll have plenty of time to answer questions in the comment sections about all the stuff I’ve written that doubtless makes no sense at all). But to start us off this morning, how about a short (<4 minutes) video from Patrick Schnable one of the two lead authors on the maize genome paper. After four years of talking about the corn genome project as well as it’s challenges and benefits, one gets very good at it.*

[flowplayer src=http://www.ag.iastate.edu/video/media/52/Sequencing_the_Maize_Genome.mp4]

See the video in it’s original context here. I’m assuming since ISU provides embedding code they’re ok with me showing it here.

*Fair disclosure, there are important reasons I may be biased in my evaluation.

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