new Multimap feature requested

Dave Matthews matthews at greengenes.cit.cornell.edu
Tue Jan 25 13:53:08 EST 1994

Hello Jean, greetings from Plant Genome II!  We have a request for a 
modification of the Multimap function for you, based on discussions with
the various groups here (all of whom are showing immense enthusiasm for 
ACEDB, by the way.)

Much of the scientific excitement in plant genomic mapping over the last year
has been about the surprisingly high degree of synteny exhibited by
relatively distantly related species, and now people want to put together
inter-species databases in ACEDB.  A problem that arises in doing this with
regard to the multimap is that frequently the 'same' (homoeologous) gene or
locus is called by different names in different species.  The multimap
currently only connects common loci by keying on the fact that they are
literally the same locus, i.e. they have the same name.

John McCarthy and I are thinking that the ideal solution would be if some
other tag within the ?Locus object could be used to determine which loci are
tied together in the Multimap.  Perhaps this tag could be chosen using an
option in options.wrm, analogous to the -Title option.  E.g.

     -Title  Tag : If present in some object of that class, the text following
                   will be used preferentially when referring to that object.

     -Multimap Tag : If present, the text following will be used as the key
                     for Multimap comparisons.

Then if we set the option '-Multimap Homoeologue_name' for example, the
following loci would be tied together when displayed on the multimap:

Locus : "cab 22L"
Homoeologue_name "Lhcb1"
gMap Petunia-6 121

Locus : "Cab-1C"
Homoeologue_name "Lhcb1"
gMap Pepper-2 143

Locus : "Lhcb1"
Homoeologue_name "Lhcb1"
gMap Tomato-2 156

Further it would be nice if the names shown on the multimap could be the 
actual locus names rather than the homoeologue names.  I.e. to allow
the user to select which map's nomenclature to display, or to show all 
nomenclatures beside their respective maps.

What do you think?

best regards,
- Dave Matthews, John McCarthy, Lisa Lorenzen, Sam Cartinhour

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