[Biojava-dev] How to read a protein seq alignment file (FASTA)

[Spencer Bliven]

Don–

I was trying to do this a while ago and got stuck in the same place. I
assumed that someone intended to implement a multiple alignment Profile,
but never got around to it. I didn't have the time to implement it properly
so I ended up just working with lists of ProteinSequences. It's possible
that this is implemented as a subclass of one of the multiple alignment
algorithms or something. If not, this is definitely a hole in BioJava that
should be filled.

-Spencer

On Fri, Jun 29, 2012 at 11:22 AM, <dnaki1 at cox.net> wrote:

>
> Hi,
> I would like to use biojava 3 to read a protein multiple sequence
> alignment file in FASTA format containing 5 sequences.
> Is this possible? It appears Profile<S,C> is the alignment interface, but
> I can't find an implementation that allows me to add more than 2 aligned
> sequences.
> Any help appreciated. Thanks
> Don Naki
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