[Biojava-l] Alignment with GAPs

[Matthew Pocock]

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

On Thursday 26 January 2006 19:51, Dickson S. Guedes wrote:
> Hello All,
>
> It is possible to make the alignment of two sequences, being that one of
> them contains GAP?
>
> I´m doing some tests with DP and the Viterbi Algorithm, but without
> success.
>
> Where can I learn about?
>
> Thank you people,
>
> []s
> --
>
> :: 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"
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