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

[Yee Man]

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
> 
>