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

Mark Johnson johnsonm at gmail.com
Mon May 21 21:21:52 UTC 2007

    That makes sense.  Is that behavior documented anywhere?  I'll
feel like less of an idiot if it's not.  8)  Either way, if you're
sure that's whats going on, I'll fix up the parser to handle that as a
split location.

> I think I know what it is.  If you mean these predictions:
> Glimmer2:
>     27    29263        6  [+1 L= 684 r=-1.187]
> Glimmer3:
> orf00001    29263        9  +1     9.60
> Glimmer2/3 are predicting a gene for a circular chromosome that
> starts at 29263 and ending at +9 (+6 for Glimmer2, which leaves off
> the stop codon).  Note in Glimmer2 detailed output the end is 29946
> and the length of the sequence is 29940, so Glimmer2 artificially
> extends the end of the sequence with part of the start.
> This is handled as a split location in bioperl and in most GenBank
> files; the above would be a location string like 'join
> (29263..29940,1..9)'.  If you switched the start and stop the
> location would be '9..29263' which wouldn't be correct (and would be
> a huge gene).
> chris

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