Re: [SO-devel] GFF 3

[Cook, M. <ME...@St...>]

Lincoln and Jannick and fellow GFF/SO wanderers,

Just recently, I've been going through this exact set of issues myself
as applied to correctly inferring SO compliant features for
splice_donor_site and splice_acceptor_site given a gene model.

I hope the following simplified example is useful to understanding the
issue, and I would appreciate your comments as to whether you agree how
I interpret the GFF3 and SO specifications in this regard.


EXAMPLE
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D

Given this simplified gene model containing two exon each being 3bp
long:

123456789
EEEIIIEEE
>>>--->>>

and given these SO definitions:
=09
	splice_donor_site: The junction between the 3 prime end of an
exon and the following intron.
<http://www.broad.mit.edu/annotation/genome/ontology/Sequence_Ontology/T
erm.html?sp=3DSSO%3A0000163>
	splice_acceptor_site: The junction between the 3 prime end of an
intron and the following exon.
<http://www.broad.mit.edu/annotation/genome/ontology/Sequence_Ontology/T
erm.html?sp=3DSSO%3A0000164>  =09

...we should encode the gene as:=20
	exon(1,3,+)=20
	splice_donor_site(3,3,+)
	intron(4,6,+)=20
	splice_acceptor_site(6,6,+)
	exon(7,9,+)

HOWEVER, if the gene codes the other way, viz.

123456789
EEEIIIEEE
<<<---<<<

...we should encode it as:=20
	exon(7,9,-)
	splice_donor_site(6,6,-)
	intron(4,6,-)=20
	splice_acceptor_site(3,3,-)
	exon(1,3,-)=20

Note that the coordinates of the exon and intron are the same in both
encodings, only the strand is different; AND, the coordinates of the
splice sites are also the same between encodings, due to understanding
"to the right of the indicated base in the direction of the landmark."
as "1 plus the indicated base, in interbase coordinates"

It is this understanding that I am trying to clarify by this example,
and would in particular appreciate confirmation that the splice sites
should NOT be encoded in the second model as:

	splice_donor_site(7,7,-)
	splice_acceptor_site(4,4,+)

Thanks,

Malcolm Cook
Stowers Institute for Medical Research - Kansas City, Missouri

________________________________

	From: son...@li...
[mailto:son...@li...] On Behalf Of Lincoln
Stein
	Sent: Wednesday, April 11, 2007 8:46 AM
	To: Jannick D. Bendtsen
	Cc: SO developers; ls...@cs...
	Subject: Re: [SO-devel] GFF 3
=09
=09
	Hi,
=09
	Zero-length and one-length features are both represented using
coordinates start=3D=3Dend. 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.=20
=09
	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.
=09
	Lincoln
=09
=09
	On 4/11/07, Jannick D. Bendtsen <jbe...@cl...> wrote:=20

		Dear Lincoln,
	=09
		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.=20
	=09
		-- 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,=20
		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 --
	=09
		From this it is clear that insertion sites, cleavage
sites etc. can be=20
		mapped onto a sequence simply by this
	=09
		ctg123 . gene 1000 1000 . + . ID=3Dgene00001;Name=3DEDEN
	=09
		But what is the region syntax for just covering one
position?
	=09
		1000 1001 will cover two positions??
	=09
		Thanks for your help.
	=09
		Best wishes
		Jannick
	=09
		--
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		Jannick D. Bendtsen
		Senior scientific officer
	=09
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	--=20
	Lincoln D. Stein
	Cold Spring Harbor Laboratory
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	Cold Spring Harbor, NY 11724=20
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