question

[Laurie G. Smith]

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
-- 
Laurie G. Smith
Associate Professor
Division of Biological Sciences 0116
U.C. San Diego
9500 Gilman Drive
Rm. 5135 Muir Biology
La Jolla, CA  92093-0116
tel: (858)-822-2531
fax: (858)-534-7108
email: lsmith at biomail.ucsd.edu