[BiO BB] custom blast server

Iddo Friedberg idoerg at cc.huji.ac.il
Wed Dec 5 12:20:57 EST 2001

Hi Joel,

I do not know the answer to your specific question. However, I am a bit
curious as to why you would like to run BLAST vs. an SQL database. You can
easily convert any data you may have to a flat format fasta file, and then
use NCBI tools formatdb to create the format which BLAST recognizes. A
table which translates from your FFFF to the SQL key fields can correlate
between the two, in case you have more than just sequence information in
your SQL database.

This is not a criticism of your choice of methods, I was just wondering
what is the application demand that makes you want to take the trouble. I
have toyed with the idea of doing something similar myself, but I always
caved in and resorted to the method above.

But hey, if you write up such a thing, that would be really cool!



On Wed, 5 Dec 2001, Joel Dudley wrote:

: Hello All,
:  I am creating a biological database for an application that I am working
: on. The database contains cDNA and AA sequences among other things. My
: application needs to perform a BLAST search on sequences in my database
: only. I would like to create my own custom BLAST server that performs BLAST
: searches on my PostgreSQL database. I planned on writing my own threading
: BLAST server in Java but I was wondering if anyone know of some tools,
: Classes, or libraries that would perform a BLAST onsequences in a
: PostgreSQL DB. Any language is welcome. If there is something close that is
: open-source I could modify the source to make it work I guess. Thanks.
: - Joel


Iddo Friedberg                                  | Tel: +972-2-6757374
Dept. of Molecular Genetics and Biotechnology   | Fax: +972-2-6757308
The Hebrew University - Hadassah Medical School | email: idoerg at cc.huji.ac.il
POB 12272, Jerusalem 91120                      |
Israel                                          |

More information about the BBB mailing list