The first thing I would suggest is running 'monitor' while the program is running. This should give you an idea is the time is being spent in your Perl script or in the database. This would help you focus your optimization effort. I worked with bioinformatic data professionally myself, and the way I would typically do these type of problems is to pull in all the data I could into memory first (hashes work wonders), process your results in memory, and then do your table inserts and updates (updates first). You want to do multiple updates and inserts in a single transaction block, but be sure to commit every so often so your backtrack space doesn't fill up.

Here are a few coding comments I have:

1. Use $INPUT_RECORD_SEPARATOR instead of $/
2. We can eliminate a lot of lexical scoping on the parse routines since the m// function returns as a list the substring matched by the capturing parentheses. If there is no match, the list item will be undef.

       # Get type. Right now, all are BAC's.
       if ($line =~ m/\b((B|Y)AC)\b/)
       {
         $type = $1;
       }
       
       # Get reference number.
       if ($line =~ m/BAC:\s*(.*)\s*$/)
       {
         $ac_id = $1;
       }
   
       # Get whether forward or reverse
       if ($line =~ m/ORIENTATION:\s*(\w)_(\d)\s*$/)
       {
         $orient = $1;
         $read_frame = $2;
       }
   [download]

   becomes

       # Get type. Right now, all are BAC's.
       ($type) = $line =~ m/\b([BY]AC)\b/; # regex change
       
       # Get reference number.
       ($ac_id) = $line =~ m/BAC:\s*(.*)\s*$/;
   
       # Get whether forward or reverse
       ($orient, $read_frame) =
         $line =~ m/ORIENTATION:\s*(\w)_(\d)/; # regex change
   [download]

3. Watch all the *'s (especially .*'s) in regex's, they may not all be necessary.

I think everything else has been said already. I'd like to reiterate the utter stupidity of the CS department not allowing you to take their classes.

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