[Gramene] Rice identifiers and orthologues

[Pankaj Jaiswal]

Dear Reena,

Instead of going to the ftp site, we have a web based tool for you to 
specifically generate your desired query results.

You can use the GrameneMart query:

-visit http://www.gramene.org
-from the search menu select 'All-GrameneMart'
-once on the GrameneMart page select choose the database 'gramene26'
-choose dataset 'oryza sativa japonica genes (TIGR5)'
-hit the 'count' button in the navigation bar in black color
-then click on 'attributes' link in the grey colored column
-open 'gene' menu and check the desired info (Ensembl Gene ID, description)
-go down and open 'external' section and check mark GO ID and GO description
-go down on same page in 'external references' and check mark any that 
you want.

-after selecting all these hit the 'result' button in the navigation bar 
in black color
-it will give you a results table.
-select your export format to get the complete results.

-in the same/different query you should be able to add orthologs from 
desired species, uniprot_IDs, TIGR_locus_ID as well, by selecting them. 
The results section will give you options to download.

Let us know if you need more help.
Pankaj

narsar01 at student.uwa.edu.au wrote:
> 
> Hi
> 
> I'm having problems finding the orthologues of my rice genes, I know I 
> can find one at a time when I put in one identifier but I have 24,000 
> TIGR LOC identifiers and I would like the Arabidopsis orthologues for 
> these but I don't know how to extract that information. In order to deal 
> with this, I looked up Arabidopsis vs. Rice in the inParanoid database 
> (which gets it's source data from gramene) and the problem I now have is 
> that the idenfiers are in another form for rice e.g. Q7F804 and I don't 
> know how to get the conversion of the identifiers.
> 
> Also, it would be really useful to be able to extract the GO annotations 
> for these rice genes too but I don't know where it is in the FTP database.
> 
> Thanks for your help.
> 
> 
> Reena Narsai
> PhD Candidate
> Plant Energy Biology
> ARC Centre of Excellence
> The University of Western Australia
> M316
> Crawley WA 6009
> Phone 61 8 6488 4434
> Fax 61 8 6488 4401
> 
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> 

-- 
Pankaj Jaiswal
G-15, Bradfield Hall
Dept. of Plant Breeding and Genetics
Cornell University
Ithaca, NY-14853, USA

Ph. +1-607-255-3103 / 4199
fax: +1-607-255-6683