Wednesday, November 22, 2006

What's a good 1Gbase to sequence?

My newest Nature arrived & has on the front a card touting Roche Applied Science's 1Gbase grant program. Submit an entry by December 8th (1000 words), and you (if you reside in the U.S. or Canada) might be able to get 1Gbase of free sequencing on a 454 machine. This can be run on various number of samples (see the description). They are guaranteeing 200bp per read. The system runs 200Kreads per plate and the grant is for 10 plates -- 2M reads -- but 2M x 200 bases = 400Mb -- so somewhere either I can't do math or their materials aren't quite right. The 200bp/read is a minimum, so apparently their average is quite a bit higher (or again, I forgot a factor somewhere). Hmm, paired end sequencing is available but not required, so that isn't the obvious factor of 2.

So what would you do with that firepower? I'm a bit embarassed that I'm having a hard time thinking of good uses. For better-or-worse, I was extended at Millennium until the end-of-year, so any brainstorms around cancer genomics can't be surfaced here. There are a few science-fair like ideas (yikes! will kids soon be sequencing genomes as science fair projects?), such as running metagenomics on slices out of a Winogradski column. When I was an undergrad, our autoclaved solutions of MgCl2 always turned a pale green -- my professor said this was routine & due to some alga that could live in that minimal world. Should that be sequenced? Metagenomics of my septic system? What is the most interesting genetics system that isn't yet undergoing a full genome scan?

Well, submission is free -- so please submit! Such an opportunity shouldn't be passed up lightly.


RPM said...

The link you gave to the 1Gbase Grant Program doesn't seem to work for me.

Keith Robison said...

Ugh, you are correct. I will fix it, but the correct linke is -- when you go there, you end up picking a country & such, and that gives you the URL I made the mistake of cutting-and-pasting -- a URL which doesn't last & probably doesn't work except for me. Something to watch in the future. KR