Not yet, I'll be setting that up this afternoon.

You beat me to the punch on that one. I was already planning it. :D

Update: Here is the original sub's run times:

Total Elapsed Time = 1135.701 Seconds
  User+System Time = 770.4718 Seconds
Exclusive Times
%Time ExclSec CumulS #Calls sec/call Csec/c  Name
 63.8   491.8 491.86      1   491.86 491.86  main::WEED
 32.5   251.1 251.10  22012   0.0114 0.0114  main::SEARCHFASTA
[download]

And here it is without the switch to grep, but keeping the sorting fixes you suggested, as well as most of your other helps:

Total Elapsed Time = 789.7615 Seconds
  User+System Time = 741.4615 Seconds
Exclusive Times
%Time ExclSec CumulS #Calls sec/call Csec/c  Name
 65.4   485.3 485.35      1   485.35 485.35  main::WEED
 33.5   248.8 248.86  22012   0.0113 0.0113  main::SEARCHFASTA
 0.96   7.120  7.120      1   7.1200 7.1200  main::INDEX_FASTA
[download]

So, removing the double sorting shaved off 6.5 seconds. It's a start.. Now, to try and shave off another 300 or so more....

Matt