Hello David,
If the sequences that you describe are proteins with the same function
but not derived from the same ancestral gene then perhaps they would be
distributed on a different portion of the linkage map. I don't know if
it is feasible in your system or what the copy number is, but if you
perform a cross you can observe how the proteins segregate and assort and or
try a complementation test if you have recessive phenotypes.
If the proteins fail to compliment in trans then they are the same gene
at the same locus, but if the proteins assort independently then they are at
different loci. If the proteins occupy the same locus then aren't they
homologous? Otherwise they have either duplicated or are not homologous
- perhaps recruited from another ancestral gene. Anyway, maybe you can take
advantage of something external to the protein's own sequence to attack
the question of homology.
Cheers,
Dan
_____________________________________________________________________________
Daniel J. McGoldrick (707) 875-2076 Lab
U.C. Davis, Bodega Marine Laboratory (707) 875-2089 Fax me
P.O. Box 247
Bodega Bay, Ca. USA 94923
-----------------------------------------------------------------------------
