[Biojava-l] create Profile from a file in biojava3

[Andreas Prlic]

Hi Dave,

BioJava does currently not allow to convert between different multiple
sequence file formats , if that is what you want to do. We have had a few
requests over time to be able to read a profile from some of the popular
multiple sequence alignment file formats. I'll add it as a feature request
on github.

Thanks,

Andreas



On Sun, Dec 21, 2014 at 11:09 PM, Michael Heuer <heuermh at gmail.com> wrote:

> Hello Dave,
>
> From what I can tell from the biojava3-alignment API
>
> http://www.biojava.org/docs/api/org/biojava3/alignment/package-summary.html
>
> and the detailed notes from Mark Chapman's GSoC MSA project
>
> http://biojava.org/wiki/GSoC:MSA
>
> I don't think you can read in an existing MSA from a file into the
> biojava3 Profile class.  You could just perform the MSA with biojava3
>
> http://biojava.org/wiki/BioJava:CookBook3:MSA
>
>
> Alternatively, in biojava-legacy there is a clustalw parser
>
>
> http://www.biojava.org/docs/api1.9.1/org/biojava/bio/program/sax/ClustalWAlignmentSAXParser.html
>
> I've never used that package though and don't know how well it has kept up
> with changes to clustalw if at all.
>
>    michael
>
>
>
>
> On Sat, Dec 20, 2014 at 3:41 PM, Dave Roe <daveroe25 at gmail.com> wrote:
>
>> I can't figure out how to create a Profile object from a MSA file (e.g.,
>> .msf) in biojava3. Any suggestions?
>> --
>> Dave
>>
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>>
>
>
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-- 
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Dr. Andreas Prlic
RCSB PDB Protein Data Bank
University of California, San Diego

Editor Software Section
PLOS Computational Biology

BioJava Project Lead
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