[BiO BB] My Protein Sequence analysis tool is taking a lot of time to complete a single database similarity search

[prathibha bharathi]

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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