Mad Prime: Hacking BLAST

Hacking BLAST

Madeleine Ball — Thu, 06 Apr 2006 03:28:00 +0100

There are increasingly many biotechnology protocols which involve hybridizing small fragments of DNA to a large pool - methods that are sensitive to cross-hybridization. (PCR is less sensitive to this because it requires a pair of matches within a reasonable space and correct orientation, and bad matches can get weeded out by the exponential growth involved.)

So how do we check for a close match? Well, usually people run BLAST. But BLAST has been designed to look for evolutionarily close matches to a sequence -- not matches close in free energy of hybridization. It's the wrong tool for the job. It penalizes mismatches too heavily, and it treats A-T and C-G bonding as equivalent.

But I didn't want to rewrite BLAST. It'd take me months or years. Well, we can hack BLAST to fit our needs. I've figured it out and wrote up a little HOWTO guide here.

"Hacking BLAST" by Madeleine

Mon, 08 May 2006 03:32:55 +0100

Thank you for posting that! I admit - it was a bit of both. I hadn't realized anyone but Chris was reading this stuff! The "hectic part" comes from this - at lab, almost four weeks ago, I came up with a really good new experimental approach. It absorbed my mind, and I couldn't really talk about it here. But it's smoothing out now that I've settled on a plan, the future work will be less thinking and more doing. So hopefully I'll be posting more. :-)

"Hacking BLAST" by Dan

Wed, 03 May 2006 13:46:28 +0100

I hope this period of silence is just due to a hectic schedule, and not throwing in the towel ... I like reading your blog, as it gives me a vewpoint into a realm of science I don't much get the chance to look at, but am still interested in. Please keep up the good work! :-)