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

Martin Gollery mgollery at unr.edu
Thu Mar 11 09:22:12 EST 2004

The Smith-Waterman algorithm is quite sensitive, but yes it is slow. Switch to 
FASTA or BLAST with some of the sequences that you have already run and see 
what you miss with your particular data- in most cases, it will be several 
percent that you will miss, but it might be worth it if it allows you to get 
the job done in a reasonable amount of time.


Quoting prathibha bharathi <prathibha_562 at yahoo.co.in>:

> 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"
>                   Thanking You,
>                                                           Prathibha.
> Yahoo! India Insurance Special: Be informed on the best policies, services,
> tools and more.

Martin Gollery
Associate Director
Center For Bioinformatics
University of Nevada at Reno
Dept. of Biochemistry / MS330

This mail sent through https://webmail.unr.edu

More information about the BBB mailing list