From: | Simon Riggs <simon(at)2ndquadrant(dot)com> |
---|---|
To: | Troels Arvin <troels(at)arvin(dot)dk> |
Cc: | pgsql-hackers(at)postgresql(dot)org |
Subject: | Re: Adding a suffix array index |
Date: | 2004-11-19 15:45:40 |
Message-ID: | 1100875810.4113.13675.camel@localhost.localdomain |
Views: | Raw Message | Whole Thread | Download mbox | Resend email |
Thread: | |
Lists: | pgsql-hackers |
On Fri, 2004-11-19 at 10:42, Troels Arvin wrote:
> Hello,
>
> I'm working on a thesis project where I explore the addition of a
> specialized, bioinformatics-related data type to a RDBMS. My choice of
> RDBMS is PostgreSQL, of course, and I've started by adding a "dnaseq" (DNA
> sequence) data type, using PostgreSQL's APIs for type additions.
>
> The idea is to try to make it practical and even "attractive" to work with
> DNA sequences in an RDBMS. My starting goal is to make it viable to work
> with sequences in the 50-500 million base range. Some may think that
> RDBMSes and long chunks of data don't match well. My opinion is that the
> increasing power of computers and RDBMS software should at some point make
> it possible to work with DNA sequences in a "normal" data management
> setting like a RDBMS, instead of solely using stand-alone tools and
> stand-alone data files. Anyways, it's an open question if my hypothesis is
> right.
>
Presumably you know about these?
http://www.ncbi.nih.gov/BLAST/
http://www.ciri.upc.es/cela_pblade/BLAST.htm
http://www.netezza.com/products/bio.cfm
I think you're right, but you'd need to have more than one application
of the data for it to be a convincing argument. Without parallelism,
your best efforts will be to equal the speed of the single-use data
structures used in BLAST.
--
Best Regards, Simon Riggs
From | Date | Subject | |
---|---|---|---|
Next Message | Tom Lane | 2004-11-19 15:57:22 | Re: Test database for new installs? |
Previous Message | Peter Eisentraut | 2004-11-19 15:45:32 | Re: Test database for new installs? |