[BiO BB] My Protein Sequence analysis tool is taking a lot of time to complete a single database similarity search
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!!
M.Sc of Cell and Molecular Biology,
Laboratory of Biophysics and Molecular Biology,
Institute of Biochemistry and Biophysics(IBB),
University of Tehran,
E-Mail: hamid at ibb.ut.ac.ir
Alt. E-mail: nikbakht at ibb.ut.ac.ir
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
> 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,
> Yahoo! India Insurance Special: Be informed on the best policies,
> services, tools and more.
More information about the BBB