One idea would be to reserve three letter names for elegans and let
everyone else go wild with names of the form: abcdefghi-n. The
choice of using Cbr-unc-4 would still be open.
My main motivation was having unique names and not hurting the C.
I guess I'm okay with this, as long as we keep the three-letter species prefix.
Eric: ...And as we heard in LA, there is no clear fog-2
orthologue, but many FTR genes in both species. How do we handle
--Well, at the moment it is not possible to tell which of all those
C. briggsae FTR genes are ortholog(s) of fog-2, because there are
only 2 species represented (we will need 4 species represented to
make this determination). But if there have been independent
duplications of FTR genes in each lineage, then there will be
MULTIPLE ORTHOLOGS for fog-2 (i.e., all the genes in C. briggsae that
share a common ancestral gene from which fog-2 derived in the
Given that, I'm willing to consider the idea of parallel
naming--one specifically relative to elegans, another independent.
... Do we really want to have to look at a correspondence table to
see what a gene does?
--God no, not parallel naming. We want to avoid synonymization
problems AT ALL COSTS. A correspondence table for orthologs would
not in any way tell you what a gene does. But it provides an
efficient database-friendly method for determining orthologs.
(Even though a good prediction is that orthologs will share function
because they share ancestry, one can only determine function by some
kind of empirical work, and orthologs could well have changed
function during evolution, or at least developmental role. Note:
contrary to popular belief systems, "COGs" are not necessarily
orthologs. Deletions of a different paralog in each genome could
easily lead (and HAS led) to mistaking a reciprocal highest BLAST
pair for orthologs.)
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