[Bioperl-l] Why does Bio::DB::GFF::Feature::gff3_string swap start and stop coordinates??

[Torsten Seemann]

> glimmer2/3 both assume the genome is circular by default (I'm
> assuming since Glimmer2/3 are used for bacterial genomes).  Acc. to
> the Glimmer3 release notes the detail file has the information in the
> header; from the Glimmer3 data used for tests:

You beat me to the reply Chris - yes, Glimmer2/3 assume circular
chromosome by default. I had forgotten about this in earlier
discussions of the new Glimmer parsers as I normally run it in
--linear / -L mode (even if I know it is circular) because it is
easier to handle, and our sequencer/assembler team usually gets the
origin of replication right.

> Command:  /bio/sw/glimmer3/bin/glimmer3 -o 50 -g 110 -t 30 ../BCTDNA
> Glimmer3.icm Glimmer3

I did a double-take here - that's the path to my Glimmer3
installation! It took me a couple of minutes to realise that you got
it from the bioperl test data I created. D'oh! :-)

> There are options available for glimmer3 (-L, -X) that specify a
> linear sequence or allow ORFs to extend past the end of the sequence
> analyzed (the latter assumes a linear sequence).

If the -L mode should produce Bio::Location::Split objects, I guess if
-X is used
it should produce Bio::Location::Fuzzy objects too...

--Torsten