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

Chris Fields cjfields at uiuc.edu
Tue May 22 01:00:58 UTC 2007

On May 21, 2007, at 7:29 PM, Torsten Seemann wrote:

>> 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! :-)

Yep, I forgot about that!

>> 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

True, didn't think about that one.  Def. something to consider adding  


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