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

[Yee Man]

On Wed, 5 Mar 2003, Aaron J Mackey wrote:

> 
> Hi Yee,
> 
> I downloaded your code, and compiled it using -O2 -Os (Mac OSX recommended
> "fastest" code, i.e. no -g).  Using your align.pl on t1.fa and t2.fa on a
> 1GHz G4, it took about 50 seconds to calculate the alignment (I used the
> Benchmark module to specifically time only your alignment algorithm, not
> any of the other code).
> 
> On the same machine, compiled with the same flags (and no AltiVec tricks),
> `ssearch34 -q -H -d 0 -3 -f 3 -g 1 -r "3/-1" -m9c t1.fa t2.fa` takes about
> 7 seconds to calculate the same alignment (although your end coordinates
> for the alignment have an off-by-one error).  Here's the alignment ssearch
> calculated: =51-1=2067-1=25-1=1711+1=5872 (= match, - query gap, + lib
> gap).

I also noticed it is pretty slow in my machine, too...

> 
> Where is the 7-fold difference in speed coming from?  Your code did run
> with 8 Mb of memory, whereas ssearch34 ran with about 16 Mb.  Are you sure
> you're actually running the dropgsw.c code?  Ahh yes, you are; I commented
> out do_work() in pgreen.c and now you only take 41 seconds (do_work() only
> calculates a score; do_walign doesn't actually require do_work to have
> happened).  So now we're down to 6-fold slower.  What else?  When I wrap
> you call to do_walign in pgreen.c with clock() calls, I see your do_walign
> does take 40 seconds.  Did you need to change anything in do_walign to
> make it work?

Sorry about the do_work. I was thinking it is needed to locate the
alignment and then pass it to do_walign to do the global alignment... I
guess do_walign does both?

I didn't change anything in do_walign. You can do a diff to it and check.
The only difference is I defined LFASTA so that calcon won't display
sequence strings that are outside of the alignment. I am not sure if it
will trigger other stuff.

Regards,
Yee Man

> 
> -Aaron
> 
> On Tue, 4 Mar 2003, Yee Man wrote:
> 
> >
> > Hi, Aaron,
> >
> > 	After some hacking, I added the code in dropgsw.c in the FASTA
> > release to my DNA Smith-Waterman module. You can download it and try it
> > out at http://www.stanford.edu/~yeeman/dsw.tgz. There are two files called
> > t1.fa, t2.fa for your testing.
> >
> > 	This implementation doesn't do frame shift or reverse complement,
> > it is just a plain alignment.
> >
> > 	I also discovered that the performance result I reported
> > for FASTA's Phil Green didn't say that you have to use the cc compiler and
> > the compiler options in the makefile. If I use gcc and then only use -g
> > option, it finishes alignment with t1.fa, t2.fa with -3 option will go
> > from 6sec to 12sec. My vanilla implementation of SW gives us about 50sec
> > with gcc and -g option.
> >
> > Regards,
> > Yee Man
> >
> 
> -- 
>  Aaron J Mackey
>  Pearson Laboratory
>  University of Virginia
>  (434) 924-2821
>  amackey at virginia.edu
> 
> 
>