Re: [SO-devel] GFF 3

[Lincoln S. <ls...@cs...>]

Hi,

Zero-length and one-length features are both represented using coordinates
start==end. One uses the ontology to determine whether this is a zero length
feature or a one-length feature. A zero-length feature will inherit from the
"junction" parent class, while a one-length feature will inherit from the
"region" parent class.

I would much rather use interbase coordinates (in which the numbers refer to
the positions between bases), but legacy requires GFF3 to use base
coordinates.

Lincoln

On 4/11/07, Jannick D. Bendtsen <jbe...@cl...> wrote:
>
> Dear Lincoln,
>
> I'm trying to parse a GFF file and reading
> http://www.sequenceontology.org/gff3.shtml left me with a few questions
> which I hope you will take the time to answer.
>
> -- snip --
> Columns 4 & 5: "start" and "end" The start and end of the feature, in
> 1-based integer coordinates, relative to the landmark given in column 1.
> Start is always less than or equal to end. For zero-length features,
> such as insertion sites, start equals end and the implied site is to the
> right of the indicated base in the direction of the landmark.
> -- snip --
>
> From this it is clear that insertion sites, cleavage sites etc. can be
> mapped onto a sequence simply by this
>
> ctg123 . gene 1000 1000 . + . ID=gene00001;Name=EDEN
>
> But what is the region syntax for just covering one position?
>
> 1000 1001 will cover two positions??
>
> Thanks for your help.
>
> Best wishes
> Jannick
>
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-- 
Lincoln D. Stein
Cold Spring Harbor Laboratory
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