Slow Query Performance from the Web

Hi All, 
 
 I'm new to this list - and I'm not sure this is the proper place to be
asking this question - but I'd appreciate any direction you can give. 
 
We have a query that runs over a view that joins together several
related physical files. We created indexes for each physical based on
the Where clause in the query and when I run it through STRSQL on the
400 - the performance is good - about 8-9 seconds.   When the same query
is passed from the web - we're running websphere on Window 2003 boxes -
it takes in the neighborhood of 1 minute 10 seconds.  
 
  We are trying to figure out what can be done to optimize it from the
web.  I realize I'm probably not giving enough information here - I just
have no clue where to start!  If any of you have any ideas I'd be
eternally grateful.
 
Thanks