Jalview Discussion List / Jalview Sequence Feature File

Dear Iga,
Thanks for your feedback and particularly for pointing out the jalview discussion list was broken. I think Jim has now answered your specific jalview question and the list is now fixed!!
Thanks again,


On 05/02/2011 17:29, Iga Korneta wrote:

Dear Professor Barton,

The Jalview Discussion Mailing List subscription web page doesn't work, so I'm not sure if the mailing list itself is working. This is why I'm writing to you - no other contact has been given.

I had a problem with the Jalview Sequence Feature File. I am running Vista and Jalview 2.6.1.. I had annotations of secondary structure for all sequences in the alignment from an external source. I used a Python script to convert these to a sequence feature file which looked just like in your documentation. This SFF didn't work, as in: upon loading onto an alignment, it loaded into the alignment (new lines were added to the alignment instead of colouring the alignment).

I created some features in Jalview, exported these to a file, and cut-and-pasted features (both colours and the features) from my file into the Jalview-created file. This worked.

I am happy that my solution worked. But could someone from your group please explain what happened? I'm not sure if it's going to work next time.

Is it because of the additional carriage marks/line end marks in Windows as opposed to Linux/Unix? Jalview has some trouble with them in other places, too, I have noticed.

With best regards,
Iga Korneta

Geoff Barton, Professor of Bioinformatics, College of Life Sciences
University of Dundee, Scotland, UK. g.j.barton@dundee.ac.uk
Tel:+44 1382 385860/388731 (Fax:385764) www.compbio.dundee.ac.uk

The University of Dundee is registered Scottish charity: No.SC015096