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

[Aaron J Mackey]

On Sun, 26 Jan 2003, Yee Man wrote:

> Finally get it running but I have to use my own scoring
>
> ssearch34 -n -q -H -d 1 -b 1 -m 0 -f 3 -g 1 -r +3/-1 t1.fa t2.fa
>
> This takes 50 sec in my machine but it is still faster than my fastest
> implmentation (1 min 3 sec). However, if I use the default scoring, it
> gives me the E() error and refuse to align. :(

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.

-Aaron

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