[bip] BLAST and FASTA performance

[Gregory Jordan]

Coincidentally, I've lately had a look at some data for these exact two
trends (figure attached, ignore the bottommost points).

The EMBL-bank database has doubled roughly every 17 months, but processor
speed (or, more precisely, transistor counts in Intel PC processors) has
been doubling every 24 months. Back in 1970, we had a cool 1-to-1
nucleotide-to-transistor ratio; now it's nearly 1000-to-1.

Of course, the only reasonable conclusion from these trends is that we are
drawing ourselves ever nearer to an inexorable suffocation under our own
overwhelming mass of data; or, more alliteratively, that these apocalyptic
asphyxiations are approaching at an alarmingly accelerating rate!

;)

greg

On Tue, Jul 22, 2008 at 12:11 AM, Andrew Dalke <dalke at dalkescientific.com>
wrote:

> It's interesting reading that searching the world's genetic data has
> taken effectively the same time for the last 15 years.  I'm assuming
> of course that's using weighted-for-inflation cost of hardware.
> GenBank size doubles every 18 months, and CPU performance doubles at
> roughly the same rate.
>
> (This coincidence is suggestive - is the growth in sequencing data
> dependent on processing power?  Eg, how much of the assembly process
> is CPU bound?)
>
> My technical optimism says that the algorithms should also be
> improving, so similarity search time should have gone down.  Given
> the number of people who have worked on sequence similarity
> algorithms, I'm surprised this hasn't happened.
>
>
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