[Bioclusters] Re: SSE2 HMMer

[Shawn O'Connor]

[David Huen writes:]
> I think the G4/G5 is clearly the best HMMer platform around 
> (excepting FPGA implementations of course).

Respectfully disagreed.  This isn't meant as an advertisement
either for ourselves or Intel, but the Pentium 4 or Xeon is
the best price/performance platform for HMMER today.  Even
given the 2Ghz G5 specs published by Apple which won't be
available until later this year. 

Although it's commercial software rather than open source, our
vectorized LDhmmsearch and LDhmmpfam for the Pentium 4 are
comparatively faster than the speedup reported for Altivec
vs non-Altivec hmmsearch and hmmpfam on a Mac. 

Obviously the G4 and G5 have freely available vectorized HMMER,
but even including the cost of our software an Intel cluster
can deliver better HMM price/peformance than a Mac cluster or
specialized hardware boxes. 

That said, Mac OS X is an excellent operating system and it
would be great to see it available on Intel or AMD in order
to really compare apples to apples. 

Shawn O'Connor
shawn@logicaldepth.com
http://logicaldepth.com