It depends on what Indu means. No mention is made of a prediction, so
all that is required may be a mapping to the PDB repository for
structural data.
Or, if a prediction is really what is required then I can suggest the
java based Jalview (www.jalview.org) tool, which can do predictions via
Jpred/Jnet.
http://www.compbio.dundee.ac.uk/www-jpred/index.html
Jalview is being developed within our lab and I was involved in the
deveopment of the latest version of Jpred.
Regards,
Chris
On 21/05/10 23:05, Mark Fortner wrote:
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<[email protected]> wrote:
Hi Indu,
BioJava current can't do secondary structure prediction....
Andreas
On Thu, May 20, 2010 at 1:00 AM, indu pandey<[email protected]>
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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