[Bioperl-l] Bio::Graphics off by one?

Dave Howorth dhoworth at mrc-lmb.cam.ac.uk
Tue Feb 21 11:50:37 EST 2006


Lincoln Stein wrote:
> When you are looking at the resolution of individual bases, a base pair at 
> position one occupies the half-open interval from 1->2, meaning that it comes 
> up to, but doesn't quite touch, the 2. For the purposes of display, 
> Bio::Graphics draws the end of the half-open interval.

I think I understand the description of what it's doing but I don't 
understand why. What is the purpose of labelling the [44,45) interval 
45, when that interval is representing the 44th discrete mer?

I'm working with proteins and domains, so I'm always at the level of 
individual residues and people frequently care about the exact residue 
boundaries, especially when the regions are short. So I need to make 
pictures that match the data.

The displayed track seems more consistent with an interpretation that 
the residues are represented by the discrete integer points along the 
line but I don't know if I'm buying myself trouble later if I try to 
adopt that interpretation.

Alternatively, is there some way to get a track with 44 intervals, 
labelled 1 to 44?

Or will I need to patch my copy of bioperl to achieve that?

Thanks, Dave


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