From: muralrj@ornl.gov (Richard J. Mural)
To: mgreese@lbl.gov
Cc: mjp@ornl.gov, 4ph@ornl.gov
Subject: Our attempt at Drosophila
Date: Wed, 30 Jun 1999 16:32:07 -0400

Dear Martin,

Here is our attempt at annotating the Drosophila adh region.
Breifly, what we have tried to do here is to find and annotate the protein
coding genes.

We began with Grail code that we had included in the X windows verison of
Grail (Grail 1.3) which is several years old and used this as a starting
poin to build a Grail-exp version for Drosophila.  This version uses the
Grail predictions and refines the results by finding homology with ESTs or
cDNAs and then constructs gene models. Obviously we didn't have a lot of
time to fine tune this system so the submitted analysis also has a bit of
hand tuning (for example if the program broke a gene in 2 pieces, we left
that result but created a record for the gene extent).  We have also put
these data up in a "Genome Channel" browser which gives easy access to the
database search results (Beauty) and can display other features like
repetitve DNA.  Two "gene names" need explaining the first "drop" is given
to a prediction we believe to be of low quality  (maybe a false positive)
the other "LE" refers to a model where the best hit against the protein
database was a Low Entropy match.

I hope we have things in proper GFF format. but you can also look at the
visualization of the result in the Genome Channel browser.  This gives
access to the gene, gene models, search of the translation of the gene
model against the protein database, the reference EST/cDNA model generated,
and the repetitive DNAs.  The "bio-popup" (the button with a callout with a
?) is very useful so do click it on.
(url=compbio.ornl.gov/droso  This will be available by Friday)

This was an interesting exercise, I look forward to discussing the results.

Sincerely,

Richard


result (*.gff) file will come as a separate mail from Doug Hyatt.

Richard J. Mural, Ph. D.
Senior Staff Scientist
Life Sciences Division
Oak Ridge National Laboratory
Oak Ridge, TN
USA
423-576-2938
FAX 423-241-1965