question

[Mary Polacco]

Hi Laurie,
We are in the final throes of building a process to place maize physical FPC
map markers onto IBM neighbors. This is in addition to refining the
genetically mapped markers on IBM neighbors where the physical map provides
a more precise ordering.

Another add to Neighbors will be the inclusion  of the Genetic map mutants,
a lower resolution map set, and with few correspondences with the higher
resolution maps, so it is really 'beware city' for those guys.

The  new neighbors should go on-line soon, and I will let you know when we
it appears at MaizeGDB. It should provide the sort of correspondances you
want to see when it gets ported into Gramene.

-mary


-- 
Mary Polacco, PhD
Research Geneticist/Curator MaizeGDB
USDA/ARS Plant Genetics Research Unit
203 Curtis Hall
Adjunct Associate Professor
Dept. of Agronomy, Plant Sciences Unit
University of Missouri
Columbia, MO 65211
Phone: 573 884 7873
FAX: 573 884 7850



On 11/21/03 9:07 PM, "Laurie G. Smith" <lsmith at biomail.ucsd.edu> wrote:

> Dear Gramene,
> 
> Your site is awesome!
> 
> However I've been struggling for the last two hours to figure out how
> to do something that seems like it should be very simple. Basically
> what I'm trying to do is to determine map locations of maize genes
> for which I know the location of the rice homolog.
> 
> Here is the basic flow of what I'm trying to do:
> 
> locate rice gene of interest based on homology to a maize gene --->
> look for markers in the immediate vicinity of the rice gene that are
> also on some sort of maize map (some are on the maize IBM 2003
> neighbors map, but the most plentiful and useful are those mapped
> onto maize FPC 2003 physical maps) -->
> find out where the maize FPC map is on the maize IBM 2003 neighbors map
> 
> I can see there are many correspondences between the maize IBM
> Neighbors 2003 map and the AGI FPC 2003 physical maps - using the
> Matrix, I can view them chromosome by chromosome, but there are
> hundreds per chromosome, so scanning these diagrams is a totally
> inefficient way to find a specific FPC and see where it is on the IBM
> Neighbors map. I figured out how to use map viewer to choose a small
> region of a maize chromosome I designate and find the FPC maps with
> correspondences in that region. But I want to search the other way
> around - to designate a specific AGI FPC 2003 map (using their names,
> like ctg514.0 or ctg1063.0) and find out whether there are any
> 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?
> 
> Thanks for any help you can give me,
> 
> Laurie Smith