[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                           
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 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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