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

[Chris Cole]

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<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