Hi!
I've studied a little bit the mime types and found the way to associate the different files to UGENE in Ubuntu (I'm using 12.04). Also, I made icons and a script. In order to work, "icons.tar.gz" and "ugene.xml" should be placed in your home folder. The script can be placed anywhere but remember to make it executable (right click/"Properties"/"Permissions"/"Allow executing file as program"). Then double click and choose "Run in terminal".

Currently, the files associated are:
*.fa
*.gb
*.aln
*.uprj
*.uwl
*.uql

Note:
The fasta and genbank icons are modified versions of this one:
http://commons.wikimedia.org/wiki/File:DNA_icon.svg

Update: forgot to add a key line to the script.

That's a great tip, thank you! I think it could even be oficially integrated into Ugene's Ubuntu build. 

Denis Kandrov wrote on Jul 18^th, 2012 at 9:59am:


Where could I get this script? As far as I understand, it is supposed to work in other linuxes as well, right?