6/24/2006

Eyes on the future: Dawg

(Population Genetics)

It's all too easy to become bogged down in the slow grind of learning and lose sight of the prize: scientific competence. As such, in addition to as many references to scientific papers as I can cram into my posts, I'll be sticking up a number of posts on things that are way too advanced for me to even seriously think about. Hey, if I was gonna let that stop me, I'd have quit learning after GCSEs ;)

Today, I'm going to look at a program called Dawg. This was created as part of the dissertation of the newly-doctorated Dr Reed Cartwright. According to the comments on that page, the dissertation is unlikely to be made publically available, but a chunk of it has been published in the Journal of Bioinformatics.

Why am I looking at this program? Because conceptually it functions in a very similar fashion to my pathetic little genetic drift simulation. Obviously it's a heck of a lot more powerful, and infinitely more biologically plausible.

So why are smart folk like Dr Cartwright working on stuff like this? Well, I think he says it very well himself in the "Motivation" section of the paper's abstract:

    Relationships amongst taxa are inferred from biological data using phylogenetic methods and procedures. Very few known phylogenies exist against which to test the accuracy of our inferences. Therefore, in the absence of biological data, simulated data must be used to test the accuracy of methods which produce these inferences. Researchers have limited or non-existent options for simulations useful for studying the impact of insertions, deletions and alignments on phylogenetic accuracy.


In short, it's hard to tell how well our methods work in biologically-realistic situations without biologically-realistic data to feed them.

The killer feature of Dawg, as I understand it, is that, unlike most such programs, it models insertion and deletion properly. To whit: rather than just inserting or deleting single bases (or ignoring so-called "indels" completely), it handles them in clusters of a biologically-realistic size. A Zipf distribution, to be precise. And I didn't know what one of those was until 2 minutes ago, but I'm sure Dawg models them wonderfully :)

I'll end here for the moment, because beyond going "ooh, shiny" there's not a lot more I can say about Dawg. However, I have a plan. As part of a computer project for my maths course, I was required to produce a program that would determine the best sequence alignment of two mutated strings (for example, the same gene in different species). Actually, that was part of what got me so interested in CB again. I still have that program, and it makes a wonderful test case for this stuff, so over the coming weeks I'll talk you through the theory behind it - and then test it on Dawg to see how well it does.

Watch this space, folks!




This is off-topic but, if any of you have trouble compiling Dawg, you're not alone. After consultation with the local compscis, I determined that one such installation problem could be fixed as follows:

In the file var.h, on lines 116 and 159 (or thereabouts) you'll see a function being used that's called "min". Replace each instance of the word "min" with "std::min".

I've just noticed that this is actually fixed in the current release (coulda sworn that wasn't the case a week ago - they must have noticed since then).

11 Comments:

Blogger Coalescent said...

Incidentally, I just attempted my first ever trackback. Since Blogger is evil and doesn't support them, I used a standalone trackback pinger called WizBang.

The trackback was to the page on Dr Cartwright's blog announcing his successful dissertation defense. I have no idea if the trackback worked - it claimed to have done so but, knowing me, I've probably ballsed it up anyway.

Anyway, on the off-chance that it gets through AND Dr Cartwright doesn't object to lamers trackbacking his blog AND anyone follows it, hello!

6/24/2006 2:42 pm  
Anonymous Reed A. Cartwright said...

Hi Coalescent,

I just found you blog. Anything I can help you with about Dawg?

You can post a comment on my blog: http://www.dererumnatura.us/.

9/21/2006 9:54 pm  
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