[BiO BB] My Protein Sequence analysis tool is taking a lot of time to complete a single database similarity search
hamid
hamid at ibb.ut.ac.ir
Thu Mar 11 09:44:46 EST 2004
Why do you use 18 tables? the relation among theses tables help to
reduce speed! I think its better to use less tables. i think most of
consumed time is for searching sequences in tables!!
/*
Hamid Nikbakht,
M.Sc of Cell and Molecular Biology,
Laboratory of Biophysics and Molecular Biology,
Bioinformatics Department,
Institute of Biochemistry and Biophysics(IBB),
University of Tehran,
Tehran,Iran.
Tel: +98-21-611-3322
Fax: +98-21-640-4680
E-Mail: hamid at ibb.ut.ac.ir
Alt. E-mail: nikbakht at ibb.ut.ac.ir
*/
-----Original Message-----
From: prathibha bharathi <prathibha_562 at yahoo.co.in>
To: bio_bulletin_board at bioinformatics.org
Date: Thu, 11 Mar 2004 09:23:36 +0000 (GMT)
Subject: [BiO BB] My Protein Sequence analysis tool is taking a lot of
time to complete a single database similarity search
> Hai all,
>
> My protein sequence analysis tool is taking a lot of time to
> complete a single request for database similarity search.My database is
> a relational database for MySQL which contains 16 tables and 2,83,366
> sequence entries.
>
> My Sequence analysis tool is currently running on a Local intranet
> server
> with 1.9GHz processor and 256MB RAM.
>
> For a single pairwise alignment it is taking around 10msecs depending
> on the length of query sequence and was taking more than 24 hours to
> complete single request with 4 threads working on 4 partitions .By
> making only 2 threads to be alive at a time working on 2 partitions(I
> partitioned my Database in to 8 based on sequence chesk sum) ,now it is
> taking around 9 hours to complete a single request for database
> similarity search.
>
> Is it really possible to reduce the time further with hardware
> configuration of 1.9Ghz and 256MB RAM.
> Or have I to go for more more powerful hardware configuration.
> Now i'm using MySQL database server and Apache HTTP server with JRun
> application server.Have i to go for more powerful application server
> than JRun .
> My implementation platform is Java and algorithm being used is"
> SMITH-WATERMAN LOCAL ALIGNMENT" algorithm.
> Thanking You,
> Prathibha.
>
>
>
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