Re: [Seqan-dev] Realigning over Amino Acids

[Hannes Hauswedell <hannes.hauswedell@fu-berlin.de>]

On 29.10.2016 03:18, Gregory Burgess wrote:
> Hi,
> 
> I'm using seqan 1.4.1.  I have a fasta file of aligned (gap characters
> included) amino acid sequences.  I would like to simply read in this
> file and use seqan's realign function over these sequences. 
> 
> I see that realign() requires a Fragment Store, but I'm not sure how to
> generate the appropriate data structures from already-aligned amino acid
> sequences.  Can someone provide a general outline of this (or another
> approach)?
> 
> Thanks,
> Greg


Dear Greg,

SeqAn-1.4.1 is not developed anymore (since quite some time now). Please
reproduce your problem with a current release and open an issue on
github.com/seqan/seqan if the problem persists.

If you don't want to use the fragment store I would recommend reading
the alignment into an AlignmentGraph and then call globalAlignment() on
that, possibly with a small band if performance is important.

Best regards,
Hannes
-- 
Hannes Hauswedell

PhD student
Max Planck Institute for Molecular Genetics / Freie Universität Berlin

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