[Jalview-discuss] Secondary Structures.

[James Procter]

Hello Jordan - thanks for your email.

Jordan Willis wrote:
> I know there is a feature where I can select my sequence and
> have jnet give me back the predictions(which is actually not working at 
> the moment for me). 
Ah. There was a problem with the JNet web service, which was recently 
upgraded; this has now been fixed.

I was wondering if you could add other secondary
> structure predictions or 
There aren't any other secondary structure prediction services available 
to Jalview at the moment, but this will change in the future.

>known secondary structure elements to your list 
> as well, like from the pdb heading.
Jalview doesn't parse the secondary structure from PDB files, but we are 
open to code contributions from anyone who'd like to implement this.

However, if you want to view secondary structure assignments for 
structures available in the PDB then you can import them using the 
sequence fetcher, and then use the DSSP das source to retrieve the 
secondary structure assignments.

 > And is using jnet the only ss predictor I can
> use that could give a graphical output?
The JNet server is - as far as we are aware - the only one that creates 
annotation in a form that Jalview can visualise. However, there is no 
reason why the output of other servers couldn't be parsed into 
annotation - the annotations file 
(http://www.jalview.org/help/html/features/annotationsFormat.html ) can 
be used to create any number of labels, protein secondary structure 
symbols, graphs and histograms below the alignment.

'hope this helps!

Jim.

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J. B. Procter  (ENFIN/VAMSAS)  Barton Bioinformatics Research Group
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