[Feedback] [Website feedback] Is Gramene in charge of the rice genome annotation?

[Dong, Qunfeng]

Hi Marcela

Thanks! So, it sounds like that Gramene release is the complete one (I.e., merged from two independent resources).

Cheers,

Qunfeng
--
Qunfeng Dong, Ph.D.
Assistant Professor
Department of Biological Sciences
Department of Computer Science and Engineering
Life Science Complex A358 (office), A440 (lab)
University of North Texas
1155 Union Circle, #305220
Denton, TX 76203-5017
Phone: 940-565-3598 (office), 940-369-5194 (lab)
http://www.biol.unt.edu/~dongq/

From: "Marcela K. Monaco" <mmonaco at cshl.edu<mailto:mmonaco at cshl.edu>>
Date: Tuesday, March 4, 2014 4:33 PM
To: Name <qunfeng.dong at unt.edu<mailto:qunfeng.dong at unt.edu>>
Cc: "feedback at gramene.org<mailto:feedback at gramene.org>" <feedback at gramene.org<mailto:feedback at gramene.org>>
Subject: Re: [Feedback] [Website feedback] Is Gramene in charge of the rice genome annotation?

Hi Qunfeng,

Thanks for the generous compliments :)
As I understand, traditionally there have been 2 parallel assemblies for Oryza sativa japonica, one by MSU (see http://rice.plantbiology.msu.edu/) and one by RAP-DB (IRGSP, see http://rapdb.dna.affrc.go.jp/).
Gramene released the first merged version of both of these assemblies which was generated by scientists of both of the above entities, and adopted primarily the gene annotations of the IRGSP group.  However, we also provide the MSU7 gene models in a separate browser track.  For more details on this, see the annotation section in http://ensembl.gramene.org/Oryza_sativa/Info/Annotation/#assembly

Marcela

PS: RAP-DB provide a gene conversion table at http://rapdb.dna.affrc.go.jp/download/archive/RAP-MSU.txt.gz


==
Marcela Karey Monaco, PhD
Gramene Project Coordinator
Cold Spring Harbor Laboratory
One Bungtown Road, Williams #5
Cold Spring Harbor, NY 11724
Phone: 516-367-8808
Fax: 516-367-6851


On Tue, Mar 4, 2014 at 5:02 PM, qunfeng.dong at unt.edu<mailto:qunfeng.dong at unt.edu> <qunfeng.dong at unt.edu<mailto:qunfeng.dong at unt.edu>> wrote:
Qunfeng Dong (qunfeng.dong at unt.edu<mailto:qunfeng.dong at unt.edu>) sent a message using the contact form at
http://www.gramene.org/contact.

Dear Gramene team:

I am always impressed by your excellent work.  Please do pardon my ignorance
question, since it is difficult to track who is doing what these days.  My
question is whether Gramene is charge of the rice genome annotations?  I know
that Gramene is doing maize for sure, but can I trust that the rice genome
annotation downloaded from Gramene is the latest official release for the
community? Or Gramene just "imported" the rice annotation from somebody else?

Thanks

Qunfeng

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