[Biojava-l] how to get secondry structure of protein

[Mark Fortner]

I seem to recall that EMBOSS has a secondary structure prediction program.
 I'm not sure to what extent it would meet your needs, but this might help:

http://emboss.sourceforge.net/docs/emboss_tutorial/node4.html#SECTION00430000000000000000

http://emboss.sourceforge.net/apps/release/6.1/emboss/apps/garnier.html
<http://emboss.sourceforge.net/apps/release/6.1/emboss/apps/garnier.html>

I also found this site which listed a number of potential solutions:
http://molbiol-tools.ca/Protein_secondary_structure.htm

<http://molbiol-tools.ca/Protein_secondary_structure.htm>Hope this helps,

Mark Fortner

blog: http://feeds.feedburner.com/jroller/ideafactory


On Thu, May 20, 2010 at 3:43 PM, Andreas Prlic <andreas at sdsc.edu> wrote:

> Hi Indu,
>
> BioJava current can't do secondary structure prediction....
>
> Andreas
>
> On Thu, May 20, 2010 at 1:00 AM, indu pandey <er.indupandey at gmail.com>
> wrote:
> > hi,
> > Is there any program in biojava to get the secondry structure of a
> protein
> > from amino acid sequence.
> > thanx and regards
> > indu
> > _______________________________________________
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> >
>
>
>
> --
> -----------------------------------------------------------------------
> Dr. Andreas Prlic
> Senior Scientist, RCSB PDB Protein Data Bank
> University of California, San Diego
> (+1) 858.246.0526
> -----------------------------------------------------------------------
>
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