markers display in e!

[Anne Lamblin (CCGB)]

Hello!

I am part of the bioinformatics group of Ernie Retzel at the University
of Minnesota and had the pleasure to meet Susan McCouch a little earlier
last year during a NSF site visit. I am in charge of coordinating
genomics data for Medicago truncatula.  Sequencing of the medicago
genome is in progress and our next step is to display that info  ( and
other type) using EnsEMBL.
We have a running implementation of e!  As you already know, the schema
needs some tailoring to accomodate plant information.

The problem that we are encountering right now is how to handle the
markers (SSR and Markers)
I looked at 2 examples:
http://www.gramene.org/gramene/map/marker_view.cgi?marker_name=RM590
http://www.gramene.org/gramene/map/marker_view.cgi?marker_name=C405

I am wondering what are the steps you took to 
	1. get this info into e! schema  (created new tables?)
	2. get it to display on the contig view.  Modification of the pipeline
job submission and display ? program used ? 
	3. does this in anyway connect to e-pcr?

All the information might be in e! or gramene documentation  and I may
very well have overlooked it since I am more of a biologist than a
programmer. I looked at the eh? pages  (positioning Cornell SSR, map
marker info,...) in gramene but did not find enough to help me put the
pieces and rationale together.  


Much of the information that we have comes from Doug Cook's lab @ UC
Davis. (SSR, primer seq, other markers..) and are of the form found in
http://www.gramene.org/microsat/microsats.txt. What I do not understand
for example is how you use that information in conjunction with e-PCR. 
Did you actually create a target database with the info in the
microsatellites file  (primers, primer seqs, BAC name, SSR name) and
point e-PCR to it?


I would welcome any help  and pointers you can pass on.
I would be most interested in the schema/tables that hold the input and
output data and the modification of the pipeline to submit jobs related
to markers mapping and display.

Thanks in advance!

Anne-Francoise

____________________________________________________
Anne-Francoise Lamblin, Ph.D.
Center for Computational Genomics and Bioinformatics
University of Minnesota
MMC43
420 Delaware Street S.E.
Minneapolis, MN 55455

Tel. (612)624-4423
Fax  (612)626-6069
lamblin at ccgb.umn.edu