[BioPython] bioperl idl

Jeffrey Chang jchang@SMI.Stanford.EDU
Mon, 20 Sep 1999 14:45:04 -0700 (PDT)

> You didn't specific if the zero of the coordinate system is
> 0 (the way Knuth intended ) or 1 (the way Watson intended).

My preference is to use a 1- based system.  It's more natural for
biologists and seems to be more popular when numbering residues.  PDB ATOM
records typically start at 1 and BLAST results are reported with the first
residue as 1.

However, it's less clear how the end index should behave.  I personally
prefer that the end is exclusive.

>  "ANDREW"  and start = 1 and end = 3, do you get: 
>  AN <-- OMG's way?

I seem to fall in OMG's camp. 

> Any way will make someone unhappy, so there's no perfect solution.