[GMOD-devel] Re: [Open-bio-l] Schema for genes & features & mappings to assemblies

[Lincoln Stein]

Chiming in here:

> > > We do need to discuss assemblies. I vote for "flat" one level
> > > assemblies

I agree.

> > >   (b) zero level (Lincoln likes this). The schema stores contigs as
> > > "features" on DNA Sequences which are chromosome length.
> >
> > But with zero level reverse-engineering is hard, if you want to, for
> > example, do a local update, right?
>
> yup

I disagree.  Once everything is mapped to zero level it becomes trivial to 
perform coordinate transformations.  Before doing a local update, you just 
map into the coordinate system of the entry.  The only slightly tricky bit is 
remembering what the local coordinate system is.

Lincoln