[DAS] "inter-base" location format

[Brian King]

Thanks, Lincoln.

--- Lincoln Stein <lstein@cshl.org> wrote:
> Hi Brian,
> 
> Interbase coordinates, also known as "0 based" and
> "half-open intervals" have 
> the following form (best viewed in a monospaced
> font):
> 
>  0 1 2 3 4 5 7 8 9 
>   A B C D E F G H
> 
> The coordinate indicates the space between the base
> pair or residue.
> The following representations apply:
> 
>   Range     Oligo
> 
>   [1,4]     BCD
>   [1,2]     B
>   [1,1]     The space between A and B
> 
> The nice feature of 0-based coordinates is that you
> can talk about
> insertions and deletions unambiguously, and
> end-start == length.  You
> can also refer to (-) strand features by reversing
> end and start,
> although this probably isn't desirable.
> 
> Code written to use interbase coordinates is notably
> free of the +1,
> -1 adjustments that you typically find in 1-based
> coordinates.
> 
> There's not much more to say than that.  BioPerl,
> BioJava, DAS, GenBank, EMBL 
> and the biological literature all use 1-based
> coordinates and that produces a 
> very strong legacy.  Jim Kent uses interbase
> coordinates in the UCSC browser.
> 


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