protein and peptide objects in acedb

Jason Martin jason at zone.org
Fri Feb 2 14:16:44 EST 1996


Ace users, developers:

I am interested in storing exon translations from gene-prediction
programs as Protein/peptide objects.  We want to do this because of
the following sitatuation that can occur at exon splice boundaries:

     SPLICE
exon1  |  exon2
ACC GAG|GAT AGG
--- --- --- ---   the 'show translation' feature would give
THR GLU ASP ARG   the correct translation for exon2, and we would be :)

but occasionally we get this:

     SPLICE
exon1  |  exon2
C CGA G|GA TAG G   the 'show translation' feature would choke on this
- --- ---- --- -   because it doesn't know what frame to translate the
. ARG GLY   *  .   second exon in.

What we would like to do is store the translation directly as a
pepetide, that we could access by going to the 'corresponding_protein'
of each exon.  Once there, we could hopefully export the peptide
as an AA sequence.  I've tried to store peptides in an analagous
manner to storing DNA features, but there doesn't seem to be
any back-end built into aCEdb for displaying the translation.

Any ideas or help would be greatly appreciated. (sorry if you
didn't view this with a non-proportional font!)

Jason


---------------------------------------
Jason Martin
Biocomputational Scientist
Sequana Therapeutics, Inc.
11099 North Torrey Pines Rd. Suite 160
La Jolla, CA 92037

(619)-452-6550 
(619)-452-6653  [FAX]
jason at sequana.com
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