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

[Yee Man]

> 
> Is that 50 second for the entire program runtime, or just for the
> alignment calculation (remember that it calculate a score first, and then
> starts over when calculating the alignment - this is a database search
> program, after all).  Run it with -d 0 and subtract that number from 50.
> 

It takes 12 sec if I run it with -d 0. As expected, it took 4x time to
calculate the alignment. 2x to find the end points and 2x to find the
alignment.

Yee Man

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