[BiO BB] remove CTL-M and Buying a bioinformatics workstation

Yannick Wurm idh at poulet.org
Thu Sep 4 08:03:04 EDT 2003

I don't have any hands-on experience with large-volume blasting, but 
you might want to have a look at Apple's new G5 computers.
The numbers shown in the "Performance Whitepaper" of june 2003 (you'll 
find a link at http://www.apple.com/lae/g5/ ) are quite impressive. 
Apple compared the performance of the dual 2GHz Power Mac G5 running 
Apple/Genentech BLAST with a 3GHz Pentium 4-based system and a dual 
3.06GHz Xeon-based system, both running Red Hat Linux 9.0 and NCBI 

A/G BLAST is an optimized version of NCBI
BLAST developed by Apple in collaboration
with Genentech. Optimized for dual PowerPC
G5 processors, the Velocity Engine, and the
symmetric multiprocessing capabilities of
Mac OS X, A/G BLAST makes a wide variety
of searches available at higher speeds.

According to the graph they show, using a word length of 40, the Dual 
G5 ran 3 million nucleotides per second whereas the Linux boxes did 
only about 0.75.

The same paper also states that HMMer runs 4 times faster on the dual 
g5 than on the dual xeon.

And Microsoft Word runs on it too :)

Are the results shown surprising? The code for A/G Blast and HMMer seem 
to be optimized for the G5, whereas the standard vanilla versions where 
used on the linux boxes. Could optimization reduce the bias against the 

Yannick Wurm

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