markers display in e!

[Steven Schmidt]

Hi Anne,

I've noticed there are some marker tables in the core database 
of ensembl 11.
We don't use them yet & don't know how to,  but 
presumably they're more useful than the old  maps
database.

-Steve

On Tuesday 04 March 2003 17:11, Anne Lamblin (CCGB) wrote:
> 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=RM59
>0
> 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

-- 
Steven Schmidt
www.gramene.org
Cold Spring Harbor Laboratory
516-367-8892