[BiO BB] help with bacterial protein sequence comparisons

[Sterten at aol.com]

hmm, I just downloaded all bacterial sequences from genbank (~20GB)
you can always easily search these files for a keyword  
(sub-protein-sequence)
or search for sets of such subsequences simultaneously
 
with viruses I did build a binary database of  16-nucleotide-subsequences
and was searching all 24-subsequences all of whose 9 subsubsequences
were marked. This was pretty fast.
 
I'm not sure yet what to do with bacteria and amino acids
 
A blast for all bacterial sequences must be quite slow  ?!?