Hacking BLAST

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.

2 thoughts on “Hacking BLAST

  1. Dan

    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! 🙂

  2. Madeleine

    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. 🙂


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