[Biojava-l] Alignment with GAPs

[Dickson S. Guedes]

Thanks Matthew,

To produce a pair-wise alignment from two un-aligned sequences and 
introduce gaps I have used the sample at "BioJava In Anger" and it runs 
successfully.

Now I need an alignment of two sequences where one of them already have 
gaps before I align.

I mean that the DP class don´t accept GappedSequence, it´s right?

[]s
Guedes

Matthew Pocock escreveu:
> If I understand you correctly, one of the two sequences you are aligning 
> contains a gap before you align them? Or do you want to produce a pair-wise 
> alignment from two un-aligned sequences and introduce gaps?
> 
> If it is the former, you want a state that emits a gap in one sequence and a 
> symbol in the other, and also advances {1,1}. I think that is easy enough to 
> set up, but can't remember the exact code. If the worst comes to the worst, 
> you can construct the distribution over {gap,Protein} using the classes 
> in .dist and then set up a SimpleState, providing the advance and alphabet in 
> the constructor.
> 
> Matthew
-- 
--
:: Dickson S. Guedes (guedes at unisul dot br)
::
:: UNISUL - Universidade do Sul de Santa Catarina
:: ATI - Assessoria de Tecnologia da Informação
:: (0xx48) 621-3200 - http://www.unisul.br
--
"Há 10 tipos de pessoas no mundo: as que entendem
  binário, e as que não entendem"