The standard AceBrowser package comes with a 'sequence' script which
produces a neat 'Sequence report' page when viewing any sequence. No such
display has been available for viewing proteins so I thought that I would
try to create one based on the 'sequence' script to complement the
standard 'tree display' view.
I have now done this and whilst the script is heavily customised for our
Arabidopsis database (AGR), anyone can have a copy if they want to.
Some example pages from our database:
The script makes use of some other customisations in our database, but
could be easily hacked I think to suit other databases.
Whilst I thought it would be fairly simple to emulate the sequence script,
I ended up spending a few days trying to copy the standard table of BLAST
homologies from the 'tree display' into a neat table like the one that
appears on the 'sequence' output. The problem being due to the fact that
for DNA sequences, you can fire off the command:
"gif seqget $s -coords $start $end ; seqdisplay ; seqfeatures"
and the 'seqfeatures' part returns a nice hash array of all the features
and homologies associated with that sequence. You can't do the same for
proteins though as there is not 'pepfeatures' command (see my previous
The solution was a lot of AcePerl navigation through the tree display (I
presume there would be a more elegant solution, but my AcePerl skills are
a bit weak really).
~ Keith Bradnam - UK CropNet (http://ukcrop.net) webmaster and
~ Arabidopsis Genome Resource (http://ukcrop.net/agr) developer.
~ Nottingham Arabidopsis Stock Centre, University Park,
~ University of Nottingham, NG7 2RD, UK. Tel: (0115) 951 3091