[Bioperl-l] An update for my DNA Smith-Waterman code

[Aaron J Mackey]

On Sun, 26 Jan 2003, Aaron J Mackey wrote:

> % ssearch34 -n -q -H -d 0 -b 1 t1.fa t2.fa
>
> This calculates scores only, no alignments; On my 1GHz G4, running
> altivec'ed SW, this takes 1.6 seconds to calculate the SW score (32767)
> (non altivec'ed on this pair with osearch34 [non-SWAT optimized] takes 5.6
> seconds)

I forgot to add the -3 switch to make it only search on the top strand (I
assume your align.pl is doing the same); so in fact, ssearch is even twice
as fast as I previously reported (at least during the database search
phase)

-Aaron

-- 
 Aaron J Mackey
 Pearson Laboratory
 University of Virginia
 (434) 924-2821
 amackey at virginia.edu