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
> 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?
>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:
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
gMap Avena-F 44.299999
gMap NABGMP-2H 58.900002
gMap Ta-Anderson-2 18.700001
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"
gMap Avena-F 44.3
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?
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