[Biojava-l] Alignment with GAPs

[mark.schreiber at novartis.com]

There is no MSA in biojava. CLUSTALW, TCoffee etc are probably much 
better.





"Dickson S. Guedes" <guedes at unisul.br>
01/28/2006 12:09 AM

 
        To:     Mark Schreiber/GP/Novartis at PH
        cc:     Biojava-l at biojava.org, Matthew Pocock <matthew.pocock at ncl.ac.uk>
        Subject:        Re: [Biojava-l] Alignment with GAPs


Hi Mark,

Ok. I´ll test it, thanks.

Curious? :) ... I´m testing somethings about progressive alignment, 
because I dont´t found how to do Multiple Sequence Aligments (MSA) using 
with only Biojava. I´m wrong?

I make some tests with strap but it´s not what I need. Have you any 
suggestion about MSA with BioJava?

Thanks all!

mark.schreiber at novartis.com escreveu:
> Hi -
> 
> I think the DP class should accept a GappedSequence. To get the result 
you 
> want you will probably need to have at least one match state that can 
emit 
> gaps. I'm curious to know why you would want to do that kind of 
alignment 
> though?
> 
> - Mark