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

Hilmar Lapp hlapp@gnf.org
Wed, 18 Dec 2002 14:08:07 -0800

Eugen, if you think we should subscribe to the Bioinformatics list at 
OReilly, you are free to state that. I think everyone on this list 
would highly appreciate it if you left at their discretion whether or 
not they want to be subscribed there.

In other words, can you please stop these frankly very annoying 

Thank you,


On Wednesday, December 18, 2002, at 12:21  PM, Eugen Leitl wrote:

> ---------- 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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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757