importing mapmaker output into acedb

David E. Matthews matthews at cs.cornell.edu
Sat Jun 5 13:59:47 EST 1993


In article <1uijviINNp6t at news.u.washington.edu> cgr at poplar1.cfr.washington.edu 
writes:
> i'm just getting started with acedb, bringing it up on a sparcstation lx
> under solaris 2.1.  i have compiled acedb and have it running.  now i need to
> start bringing in our poplar data to create our poplar database, voxpop.
> 
> i can see how to bring in our existing bibliographies and am working on that.
> i don't see how to bring in our mapmaker output.  can anyone provide some
> advice on this?

>thanks much!
>
>---
>carl g. riches
>college of forest resources	    internet: cgr at poplar1.cfr.washington.edu
>university of washington ar-10	    voice:    206-543-2764
>seattle, wa 98195		    fax:      206-543-3254

Mapmaker output (ie linkage groups) is loaded into acedb as a list of Locus
records, each with a value for the tag "gMap".  The value is a pair: 
?Chromosome Float
giving the name of the Chromosome object and the position in centimorgans or
whatever your units are.

An easy way to see some examples would be to look at the Gopher server
"GrainGenes, the Triticeae Genome Database".  It's on the list of All the
Gopher Servers in the World.  Pick menu choice 2, "Search the GrainGenes
Database", and search for "gmap".  This will list several interesting kinds
of objects including Locus's.  E.g.

Locus : CDO64
RFLP
Chromosome_arm   2
gMap     Avena-F 44.299999
gMap     NABGMP-2H 58.900002
gMap     Ta-Anderson-2 18.700001
Probe    pCDO64
Linked_QTL       Sprouting 4
Data     Diploid Oat, Cornell
Data     Barley, SxM
Data     Wheat sprouting markers

This Locus is mapped on three different chromosomes, Avena-F etc.  In
GrainGenes the Mapmaker input data (which Brad mentioned as being included in
the "F2_data" class) are in a class called "Map"; these are listed in this
locus record under the tag "Data": "Diploid Oat, Cornell" etc.  You'll find
them on that same list of hits from the Gopher search.

The load-file (.ace) entry to load the part of this information for one
of the maps would be,

Locus : "CDO64"
RFLP
gMap Avena-F 44.3
Probe pCDO64
Data "Diploid Oat, Cornell"

Hope this helps,
- Dave Matthews
  matthews at greengenes.cit.cornell.edu


P.S. By the way, many of us have had no experience with Solaris 2.x, but we'd
been under the impression that acedb would have problems with it.  Any
comments about special obstacles you had to deal with?
- Dave




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