[Bioperl-l] [Bioinformatics] iPod and A/G BLAST (fwd)

[Eugen Leitl]

---------- Forwarded message ----------
Date: Wed, 18 Dec 2002 12:46:56 -0700
From: Nathan Torkington <gnat@oreilly.com>
To: bioinformatics@labs.oreilly.com
Subject: [Bioinformatics] iPod and A/G BLAST

There's an interesting article at:
 http://www.apple.com/pro/science/gilbert/

It's about the guy who used his iPod to transfer the genome between
machines.  I know, we all thought "boring, that's what gigabit
ethernet is for".  But he goes on to talk about some work he did with
the Apple/Genentech port of BLAST to the G4 PowerMac.  It uses the
Altivec vector coprocessor and he sounded tickled with his results:

  "I got to thinking," Gilbert says, "I wonder if that linearity
  continues. What if I cranked this thing up to word sizes of 200?
  That would certainly save the day. So I hopped on my Mac, pulled
  down the A/G Blast, spent about an hour indexing the genome a
  different way. And I said `This is either going to work or not going
  to work.' I tested a word size of 250 for my first shot. The test
  was done in two minutes, much to my disbelief. So I said, `Well,
  that must not have worked,' Yet when I examined the output, A/G
  BLAST had indeed found the right hunk of DNA. Things started getting
  very exciting at that point."

  Gilbert then slowly brought the word size down to make sure he
  wasn't losing any sensitivity.  "A/G BLAST found the same gene
  region. Whether I used a smaller word size or a larger word size, I
  would find the same piece of DNA. That was very encouraging. And
  just for giggles, I cranked it way up, too. I think at one point I
  got A/G BLAST to run a test in 19 seconds, which is just beyond
  belief."

I, of course, am interested because he used Perl :-)

Nat
[Biocon 2003, Feb 3-6 in San Diego, http://conferences.oreilly.com/bio2003/]

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