Rice gene annotation

[Lenny Teytelman]

Dear Thomas,

There are two distinct gene prediction sources in Gramene.  The "Submitted
Transcript" is parsed directly from the GenBank entries of the individual
BAC/PAC sequences and the "Fgenesh Transcript" track is from Fgenesh
predictions.

As for the "best source" of the annotation data, it depends on what you
deem the best.  The GenBank predictions are from the sequencing centers
and are not all from the same prediction protocol.  These might be better
or worse than the Fgenesh predictions from Gramene, but they also are only
available for phase 3 clones.

The Fgenesh predictions are available in Fgenesh output format at:
ftp://ftp.gramene.org/pub/gramene/protein/sequence/riceseq_fgenes_predictions_120402.dat.gz

Regards,

Lenny Teytelman

> Dear colleague,
> 
> I have two questions regarding the data of the rice genome in the Gramene 
> database base:
> 1) From which source are the gene predictions derived in your database? Are 
> they from GenBank, TIGR, your own predictions or is a combination?
> 2) Which is the best source to download the entire set of annotation data? 
> Are they available in xml format?
> 
> Thanks for you help in advance,
> 
> Thomas
> 
> 
> 
> 
> Thomas Girke
> Center for Plant Cell Biology (CEPCEB)
> Department of Botany and Plant Sciences
> University of California
> Riverside, CA 92521
> 
> E-mail: thomas.girke at ucr.edu
> Website: www.cepceb.ucr.edu
> Ph: 909-787-2469
> Fax: 909-787-4437

-- 
Lenny Teytelman
Cold Spring Harbor Laboratory
516-367-8864
teytelman at cshl.org