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

Chris Fields cjfields at uiuc.edu
Mon May 21 20:35:41 UTC 2007

On May 16, 2007, at 2:11 PM, Mark Johnson wrote:

> On 5/8/07, Chris Fields <cjfields at uiuc.edu> wrote:
>> I believe all seqfeature location coordinates are designed to have
>> start < stop for consistency; in cases where the strand matters (CDS,
>> gene, etc.) then the strand is set to 1 or -1.  When start > stop,
>> the two are reversed and the strand is flipped; at least that's the
>> way locations are set up in BioPerl.
>> chris
>     Oh yeah?  I always tend to ensure that (start < stop), regardless
> of strand, when working with sequence features...the other day, I
> caught Glimmer2 emitting a prediction on the plus strand with start >
> stop.  I was going to work up a patch for the parser, but I wonder,
> should I just force everything to start < stop?  Or only predictions
> on the plus strand?  Should all the parsers for all the ab initio
> predictors ensure they emit features with coordinates like this?

Odd that it would predict a start > stop on the plus strand, though  
it may be corrected in Glimmer3.  Does the same prediction show up in  


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