[Bioperl-l] Re: Added Phil Green's Smith-Waterman to my module

[Aaron J Mackey]

On Wed, 5 Mar 2003, Yee Man wrote:

> 	I think I figured out why it is so slow. The one you got is with
> -d 0 which calculates score only. The default behavior of my code is
> like:
>  ssearch34 -3 -n -q -H -d 1 -b 1 -m 0 -f 3 -g 1 -r +3/-1 t1.fa t2.fa

No, I did -m 9c which is like -d 1 except it doesn't spam my screen with
output.

And when I run the command line you gave, I get the same 7 seconds of
alignment calculation, and still 40 with yours.

> 	This gives me exactly the same time as I run ssearch34. So I
> believe my implementation is correct after I removed call to do_work.

I'll look into it soon, but I encourage you to "double check":

% /usr/bin/time perl -I./blib/lib -I./blib/arch align.pl t1.fa t2.fa > /dev/null
       41.43 real        40.87 user         0.21 sys

[ this includes about 1.5 seconds of Perl "overhead" ]

% /usr/bin/time ../facurr/ssearch34 -3 -n -q -H -d 1 -b 1 -f 3 -g 1 -r +3/-1 t1.fa t2.fa > /dev/null
       10.43 real        10.40 user         0.03 sys

[ This includes about 2.5 seconds of "search" time ]

-Aaron

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