Wednesday, December 10, 2008

Web Wednesday

The DRSC team recently sifted through a lot of websites to compile a first draft of a links page

The idea was to create something helpful for screen hit follow-up. Suggestions for additions are welcome.

Two sites I've stumbled on just this week are DroSpeGe and AAA (for Assembly, Alignment and Annotation; the figure shown here is from their home page). 

Both sites have information about the twelve Drosophila genomes that were published just over a year ago in Nature.

The D. melanogaster genome was published in Science while I was a postdoc (Adams et al. 2000). I still remember the excitement it generated at that year's fly meeting (ADRC). And the scramble to get a copy of the commemorative jigsaw puzzle (or was it a mouse pad?) that was produced to mark the occasion.

At that time, it was possible to compare D. mel sequence with at least partial sequence of the human genome. Sites like Homophila report aspects of those findings. 

Now, we can make different use of the twelve genomes to find sequence elements conserved over much shorter spans of evolutionary time.  

You can BLAST the sequence data here, at FlyBase or at NCBI. And if you're more interested in the actual beasts, you can order them at the fly species stock center, now at UC San Diego.

Direct impact on fly RNAi screening?  

Hard to say. It seems doubtful that we'll have cell lines and dsRNA libraries with which to probe these other species any time soon. And one might be hard pressed to argue that we'd learn much more via that route then we are learning already with RNAi assays in D. mel.

But that's an extremely limited view of the utility of the sequence. The availability of these genomes will certainly inform studies in D. mel--and broader research fields--more generally. And that's a big plus.

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