bench query from Gramene

[Immanuel Yap]

On Mon, Aug 26, 2002 at 03:56:10PM -0400, jingyu at dnalandmarks.ca wrote:
> Dear Gramene curators,
> 
> I wish I could get a table that contains below information from Gramene:
> 
> 1. MarkerName (only from map JRGP RFLP 2000) ,
> 2. MapName,
> 3. LinkageGroupNumber,
> 4. LocusName,
> 5. PositionOnMap,
> 6. GenomeView(s) - e.g. clone name(s) in contigview
> 
> For example, if for markers V32,G107:
> --------------------------------------------------------
> Marker  Map               LG  Locus  Position   Clone
> --------------------------------------------------------
> G107    "JRGP RFLP 2000"  1   G107   -1.5       AP002909
> G107    "JRGP RFLP 2000"  1   G107   -1.5       AP003233
> RZ543   "JRGP RFLP 2000"  1   V32     8.7       AP002909
> RZ543   "JRGP RFLP 2000"  1   V32     8.7       AP003233
> --------------------------------------------------------
> 
> The No. 1-5 seems can be gained from Marker Search of Gramene, but it is
> _very_ slow so that I doubt whether I can really get it if through internet
> - I tried for only 200 markers two hours ago and nothing hasn't shown up
> yet on my screen!
> 
> And for No. 6 , I wish to bench get them. So far I only can get the info
> for one marker each time by clicking on "Marker Details"...
> 
> Could you help me to obtain such info in one table?
> 
> Thanks in advance,
> 
> 
> Jing

Jing,

I think you mean "batch" query.

You can FTP the map positions for all the genetic maps in Gramene from
this URL:

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

If you just want the JRPG RFLP 2000 map specifically, you just need to
click on RJ_00.dat.  See the README file for details.

As for the corresponding clone names, I don't think that there is
currently a way to do this by batch in Gramene.  I agree that it would
be a convenient feature to have.  We at Gramene are actually
discussing how this might be implemented.

I note that this same information is available on the JRGP website:

    http://rgp.dna.affrc.go.jp/publicdata/geneticmap2000/index.html

including the associated clone names.

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