[BioPython] bioperl idl
Tue, 21 Sep 1999 12:49:33 -0700 (PDT)
--- Jeffrey Chang <jchang@SMI.Stanford.EDU> wrote:
> > You didn't specific if the zero of the coordinate
> system is
> > 0 (the way Knuth intended ) or 1 (the way Watson
> 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.
Speaking from a biologists perspective, if I ask for
1-3 of the sequence 'atgtg' and get anything but 'atg'
I'm gonna be pissed. (But not in the British sense.)
As a person, I'll go either way as long as we just
pick one and go with it.
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