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

[Andreas Prlic]

Is the problem that the SimpleProfile method makes it difficult to
re-create an instance with custom data, because there are no
set-methods?

Andreas


On Mon, Jul 2, 2012 at 9:28 AM, Spencer Bliven <sbliven at ucsd.edu> wrote:
> 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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>
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