question

[Ken Y. Clark]

On Fri, Nov 21, 2003 at 07:07:34PM -0800, Laurie G. Smith wrote:
[...]
> markers on it that are also on the maize IBM Neighbors map.  In other 
> words, for any given FPC map I'm interested in, how can I figure out 
> whether and where it maps onto the maize IBM Neighbors 2003 map?

Laurie,

I'm sorry this is proving difficult for you.  I will take a stab at
answering your question since I wrote the comparative map software;
however, I'm not a biologist, so my answer may be incomplete.  That
said, I wonder if you shouldn't start off restricting the matrix view
to the "Maize-IBM Neighbors 2003" map set like so:

    http://www.gramene.org/cmap/matrix?species_aid=;map_set_aid=ibm2n

>From there you can see that the number of correspondences from any of
the physical map sets to each of the chromosomes of maize.  Clicking
on the numbers in the matrix will take you to a view where a maize map
is the "reference" map and the FPC contigs line up where the
correspondences exists, like so:

    http://www.gramene.org/cmap/viewer?ref_map_set_aid=ibm2n;ref_map_aid=ibm2n1;comparative_maps=1%3dmap_set_aid%3dcf03

That can be confusing to look at, so perhaps you'd like to drop off
the contigs with only 1 correspondence to the reference map.  Just
indicate this as the "Min. No. Correspondences" argument, like this:

    http://www.gramene.org/cmap/viewer?ref_map_start=-55.80&ref_map_stop=1272.50&highlight=%22txa6085%28C%29%22%2C%22txa6085%22&image_size=small&font_size=small&image_type=png&label_features=all&collapse_features=0&min_correspondences=2&ref_map_set_aid=ibm2n&ref_map_aid=ibm2n1&comparative_maps=1%3Dmap_set_aid%3Dcf03&flip=&data_source=Gramene

Does that make it easier to find what you're interested in?

ky