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

[Aaron J Mackey]

I'm sorry, that was what I said but not very clearly: -3 halves the
"database search time", which of course only calculates scores, not
alignments.

The 48 to 42 second improvement you see when showing one alignment is only
due to the search phase going from 12 to 6 seconds.  There's no way to get
ssearch to only do an alignment without a search.

-Aaron

On Tue, 28 Jan 2003, Yee Man wrote:

>
> Hi Aaron
>
> I tried the -3 option on my machine. It does halve the time if you only
> calculate the score (from 12 sec to 6 sec). However it only improve the
> alignment time from 48 sec to 42 sec. The memory usage goes from 17MB to
> 15MB.
>
> Regards,
> Yee Man
>
> On Tue, 28 Jan 2003, Aaron J Mackey wrote:
>
> >
> > 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
> >
> >
>

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