bench query from Gramene

[Immanuel Yap]

On Tue, Aug 27, 2002 at 03:11:27PM -0400, jingyu at dnalandmarks.ca wrote:
> Yes, i can get a table include both map positions and clones from there,
> but the clone info is from rgp rather than that from gramene, which is
> different.  For example:  for  marker R3309 on chromosome 2 (position 150.5
> cM), rgp gives clone as D39309 and AU032043, but gramene gives clones as
> AP004081.

Ah yes, I didn't look closely enough.  AP004081 is a genomic BAC
sequenced by the IRGSP.  The other two are non-IRGSP sequences.

> Is there a way to query from Gramene to obtain a table includes both map
> positions and clones from gramene (such as that can possibly get from
> tablemaker if from acedb) through internet?

Upon further poking around in Gramene, I discovered this FTP directory:

    ftp://brie.cshl.org/pub/gramene/insilico_data/

I think you want the file called final_markers_contigs_020502.dat.gz
See the README file for more information.  The file doesn't have
genetic map positions, though.  I don't think there's any way (yet!) 
in Gramene to get the kind of table you're looking for.

Regards,
Noel
-- 
Immanuel V. Yap <ivy1 at cornell.edu>
Department of Plant Breeding and Biometry, Cornell University
G15 Bradfield Hall, Ithaca, NY 14853
Phone: 1-607-255-3103
http://www.gramene.org