[Bioperl-l] Re: Smith-Waterman question

[Yee Man Chan]

t1, t2 are both DNA sequences. Their alignment has nothing to do with
BLOSUM62... To verify your score, I suggest you run ssearch34 from FASTA
package.

Yee Man

On Thu, 28 Aug 2003, Ahmed Moustafa wrote:

> Hi Yee,
> 
> I was testing my implementation of Smith-Waterman algorithm with your t1 
> and t2 sequences. I'd like to verify the alignment score with you. Mine 
> was 56101.00 with BLOSUM62, open gap 10.0 and extend gap 0.5.
> 
> Could you please send me your score?
> 
> Thanks in advance!
> Ahmed
> 
> -- 
> Ahmed Moustafa
> Programmer/Kaiser Permanente
> 
>