[Biojava-l] Multiple sequence alignment

[Matthew Pocock]

So you want to be able to take 5 alignments to a
single profile HMM and produce a full alignment? I
would use GappedSymbolList or GappedSequence to manage
inserting gaps. Then, start with one of the
alignments, take another, insert gaps so that their
state-paths match up, then take the next, and so on.
These profiles don't have loops, right?

Matthew

 --- hlr02 at doc.ic.ac.uk wrote: 
> Hi,
> 
> I am aligning a set of sequences to a profile HMM. I
> would like to convert the 
> individual alignments into one (multiple sequence)
> alignment object. I tried to 
> build a new map for my msa by retrieving the
> sequence symbollist from the 
> statepaths and the sequence names. The problem with
> this approach is that the 
> symbollists differ in length and the alignments
> haven't been 'zipped' to take 
> redundant gaps into account.
> 
> I was wondering if biojava supports conversion of a
> set of alignments into a 
> multiple sequence alignment so that all alignments
> will have the same length.
> 
> Thanks,
> 
> Henry Romijn 
> 
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