[BiO BB] custom blast server

Joel Dudley Joel.Dudley at DevelopOnline.com
Wed Dec 5 12:37:21 EST 2001

  Here is the deal. I am assuming that you suggest that I dump all my
sequences, format them, and use the BLAST executable provided by NCBI,
right? I thought about that too. However, The application is going to make a
BLAST request over the internet and the BLAST server needs to thread (so we
can handle many concurrent connections) and return the BLAST results to the
application when the search is complete. I could make a wrapper type server
in Perl, but I think that is a bad idea. I would like to have something
cleaner. Ideally I would like to have a Threading server that handles BLAST
requests via XML RPC or something like that and integrates better with my
application. Am I making any sense here?

- Joel

-----Original Message-----
From: Iddo Friedberg [mailto:idoerg at cc.huji.ac.il]
Sent: Wednesday, December 05, 2001 10:21 AM
To: 'bio_bulletin_board at bioinformatics.org'
Cc: Joel Dudley
Subject: Re: [BiO BB] custom blast server

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
: 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
: 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                                          |

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