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,


On Sun, Jan 25, 2009 at 3:11 PM, James Procter <> 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 ) 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.

J. B. Procter (ENFIN/VAMSAS) Barton Bioinformatics Research Group
Phone/Fax:+44(0)1382 388734/345764
The University of Dundee is a Scottish Registered Charity, No. SC015096.