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
"Dickson S. Guedes" <[EMAIL PROTECTED]>
Sent by: [EMAIL PROTECTED]
01/27/2006 04:49 AM
To: Matthew Pocock <[EMAIL PROTECTED]>, [email protected]
cc: (bcc: Mark Schreiber/GP/Novartis)
Subject: Re: [Biojava-l] Alignment with GAPs
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"
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