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

[Yee Man]

> I haven't been able to reproduce that effect; what version of ssearch are
> you using (what does the version string say?)
>

I am running:
 version 3.4t20 Nov 10, 2002

with commnad like

ssearch t1.fa t2.fa

Then it gives me this error:
 Smith-Waterman (PGopt) (3.39 May 2001) function [+5/-4 matrix (5:-4)],
open/ext: -12/-4
 Scan time:  8.940
Enter filename for results []: h
 How many scores would you like to see? [20] 
!! No library sequences with E() < 2

I repeated the same thing with more parameters:
ssearch34 -n -q -H -d 1 -b 1 -m 0 t1.fa t2.fa

but I still get an error:
 Smith-Waterman (PGopt) (3.39 May 2001) function [+5/-4 matrix (5:-4)],
open/ext: -12/-4
 Scan time:  8.970
!! No library sequences with E() < 1e+07

Why is that?

Regards,
Yee Man