[Bioperl-l] Map Manipulation and Genetic Analysis

Jason Stajich jason@chg.mc.duke.edu
Wed, 17 Jan 2001 17:07:29 -0500 (EST)

Eric - 

Heikki and I had batted around talking about MarkerI for describing
Markers which can be used to build maps.  I have some code that I am using
for some analysis which I am happy to donate when it is finished.  It
doesn't do much to represent maps other than assume that markers with the
same mapid are part of the same map (data is stored in db).  But I think a
good representation of Markers first and then Maps would be very good for
bioperl and those trying to bridge the gap between genetic analysis, maps,
and sequence based investigation.

On Tue, 16 Jan 2001, Eric Snyder wrote:

> Hello BioPerl Folks,
> I was thumbing through the BioPerl modules list and noticed that there
> was not any coverage in the area of processing (non-sequence) maps and
> genetic data.  I am working on some programs for processing physical
> and genetic maps, as well as genotypic and phenotypic data.  I was
> wondering, is there any interest in these areas in the BioPerl
> community or, have I overlooked previous work on these things?
> I know of some of the stuff that Lincoln Stein has done (on ACEDB, RH
> mapping, etc.) but I have not seen anything in the form of reusable
> software components for basic map manipulation, comparison, etc.  Nor
> am I aware of modules for manipulating raw data for genetic analysis.  
> I am fairly new to working with genetic data.  I would be interested
> in hearing of leads in this area.  However, if it is not already done,
> I would be willing to write it in the context of BioPerl.
> Cheers,
> Eric E. Snyder
> Associate Professor
> Pennington Biomedical Research Center
> 6400 Perkins Road
> Baton Rouge, LA 70808-4124
> Phone:  (225) 763-3185
> Fax: (225) 763-2525
> Cell: (225) 235-6271
> Email: eesnyder@pbrc.edu 
> ICBM: N 30 24'14.0", W 91 07'20.0"
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Jason Stajich
Center for Human Genetics
Duke University Medical Center