[Biojava-l] Questions about simple alignment

[MoonTigress Chiko]

Hi everyone,

I'm quite new to biojava and to the mailinglist so I'm not sure if my 
question has been answered before, although I did look into the older 
mailinglist entries and found nothing...

Anyway, I'm writing a little java programn to align two protein sequences, 
using the pam250 matrix. So there is my first question, is the pam250 matrix 
already loaded in biojava? (like with the needleman algoritm, which has its 
own class)
I looked al over the API en cookbook and wherever on google, but I couldn't 
find any information on this. If not, how can I make the simple alignment 
use the pam250 matrix?

My second question is how to make penalty's in the alignment. Like a 
origination penalty (of 8) and a length penalty (of 2). It seemed impossible 
to scan the entry string (given in a textfield) for the existance of an '-' 
and then add the penalty's so that's not an option. How can I do it 
otherwise?

TIA!

Chiko.

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