Gramene comparative maps (WAS: Re: [Fwd: Ontology Submission from gramene.org])

[Immanuel Yap]

On Fri, Jun 28, 2002 at 10:32:40AM -0400, Pankaj Jaiswal wrote:
> "H. E. Shashidhar" wrote:
> > 2.  How can I compare the different rice maps with reference to
> > relative position of markers.  I say a presentation by Robert (of
> > IRRI Biometrics division recently in a workshop in Philippines).
> > Does Gramine support such a tool?
> > 
> 
> I will ask our comparative map curator, Noel Yap to specifically answer this
> query.

You can compare two maps using the Gramene Map Viewer:

    http://www.gramene.org/maps/viewer

First, select a mapping study from the "Ref. Study" drop-down, then
select a linkage group from the "Ref. Map".  This will show you the
linkage map for that one study.  For example, you can see chromosome 1
from the Japanese RFLP map:

    http://www.gramene.org/maps/viewer?reference_map_id=25&prev_reference_map_id=&reference_map_study_id=2

You can then select another map to compare to the reference map.  The
"Comp. Map" listbox shows all other maps (both physical and genetic)
in Gramene that have some correspondence with the reference map.
Select a map from the list and click on the "Show map" button.  For
example, you can compare chromosome 1 from the Japanese map with the
corresponding chromsome from the Cornell RFLP map:

    http://www.gramene.org/maps/viewer?start=0&end=181.8&highlight=&comparative_map1=genetic_map_id%3D1&show_only_concordant_contigs=1&image_height=400&font_size=small&image_type=png&reference_map_study_id=2&reference_map_id=25&start=0&end=181.8&highlight=&flip=

We will soon have the capability to compare more than two maps at a
time.  We'll post a news item on the Gramene home page when that
happens.

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