[Bioclusters] Apple/Genentech BLAST

[Ivo Grosse]

Hi,

in February I ignored the announcement of an Apple-optimized version of 
Blast that could run 5 times faster on a 1.0 GHz G4 than the standard 
NCBI version of Blast runs on a 2.0 GHz P4, but now, after Apple 
started building dual-G4 1U rackmountable servers, that announcement 
becomes interesting.

                         Apple/Genentech BLAST provides improved 
accuracy and
                         speed over the standard NCBI BLAST, depending 
on search
                         parameters such as the nucleotide 
match-length. For certain
                         common searches this version enables a dual 
1-GHz Power
                         Mac[tm] G4 computer to deliver more than five 
times the
                         performance of a comparable 2-GHz Pentium 
4-based
                         system running the standard NCBI BLAST. 

                         "Apple and Genentech have dramatically 
increased the
                         performance of an important tool that 
biomedical researchers
                         use every day," said David Botstein, Ph.D., 
professor and
                         chair of the Stanford University Genetics 
Department. "I'm
                         impressed and delighted that a machine that a 
regular
                         scientist can afford and run, such as the 
Power Mac G4, is
                         as fast, or faster, than the industry standard 
BLAST running
                         on more expensive machines."

I wonder if anyone could do the following benchmark (on a dual-G4) and 
publish the results?

Blast human chromosomes 21 and 22 (query sequences) against the genome 
of pufferfish (database).  Use default parameters for blast (i.e., no 
word length of 40, etc.) and an E-value of 10^{-4}.  If possible, 
submit both jobs independently and simultaneously, so that one CPU is 
blasting chr 21, while the other CPU is blasting chr 22.  Thanks!

Ivo

http://www.apple.com/pr/library/2002/feb/07blast.html
http://developer.apple.com/hardware/ve/acgresearch.html
http://www.apple.com/pr/library/2002/feb/07blast.html
http://www.newsfactor.com/perl/story/16364.html
http://maccentral.macworld.com/news/0202/07.blast.php
www.creativeresources.net/pdf/L18299B_PMG4_DS.pdf