[Jalview-discuss] Message

[Massassi Pepito]

Hello James,

I would like to know if there is any improvement for my case (coloring the
secondary structure information).

Otherwise you can give some hints, I could try some programming.

Thanks for your help,
Massassi

On Sun, Jan 25, 2009 at 3:11 PM, James Procter <jimp at compbio.dundee.ac.uk>wrote:

> Massassi Pepito wrote:
> > For any reason or others, all my messages about improving Jalview
> > appeared to be erased.
> It sounds like a problem with your email. The jalview-discuss mailing
> list has been moved to a new server, but the archives should all still
> be intact. You must, however, post to the mailing list in order for your
> emails to be archived.
> >
> > I would like to know, if anything happened.
> I'm afraid I don't have any spare time to implement the format that you
> want. I did consider constructing an example to show you how it could be
> done using the annotation file, but it sounds like you want to be able
> to display secondary structure symbols *under each sequence* in the
> alignment. This is not possible with jalview at the moment - although
> features imported using GFF or a jalview features file can be used to
> highlight secondary structure as different coloured regions on each
> sequence (e.g. the secondary structure from Uniprot records in the
> default feredoxin alignment example that is displayed in the
> application). Secondary structure annotation (such as the annotation
> shown in the applet example http://www.jalview.org/examples.html ) can
> only be displayed at the bottom of the alignment.
>
> I have made a note of your request, and hopefully someone will find the
> time to implement the format you described and the additional
> visualization capability.  But there are no guarantees since we don't
> have any funding to maintain jalview at the moment.
>
> again, thanks for your email.
> Jim
>
> --
> -------------------------------------------------------------------
> J. B. Procter  (ENFIN/VAMSAS)  Barton Bioinformatics Research Group
> Phone/Fax:+44(0)1382 388734/345764  http://www.compbio.dundee.ac.uk
> The University of Dundee is a Scottish Registered Charity, No. SC015096.
>
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