[Bioclusters] quick look see at fractal computing.

James Cuff jcuff at broad.mit.edu
Thu Feb 23 15:48:09 EST 2006

On Wed, 2006-02-22 at 17:48 -0700, Nick Robertson wrote:

> If you could please post your input query and the results file produced by MPT, 
> I will re-run this experiment and attempt the reproduction of these results. 



The result file has the same name as the files on your system I ran a
couple of hours ago.  It's a pretty noddy test, I don't have the time to
do any more sorry.  I see two issues that could stop uptake by a wide
audience right now:

1. The sub alignments are not being reported.  This will make your code
go fast, but having given the data a quick once over I'm sure this is
where you are missing alignments.

2. The blast format output could not be parsed without modifying it
first, although this is easy for you to fix.  I only noticed it when
starting to check the results.  Sorry most bioinformatics is parsing and
data munging, boring but it needs to be done.

Anyway, the results are up for all to see, hope you can work round these
wrinkles.  Thanks for being open about this Nick, I'm sure you'll get
through the teething issues, it's still early days for the product.

I'm all done, if others in the group want to take this further then
cool, but I'm bowing out now.



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