Re: [SO-devel] GFF 3

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Yes, interbase sites are to the right of the indicated base, regardless of
the strandedness of the feature that you are mapping.

Lincoln

On 4/11/07, Cook, Malcolm <ME...@st...> wrote:
>
> 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
> ============================
>
> Given this simplified gene model containing two exon each being 3bp
> long:
>
> 123456789
> EEEIIIEEE
> >>>--->>>
>
> and given these SO definitions:
>
>         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=SSO%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=SSO%3A0000164>
>
> ...we should encode the gene as:
>         exon(1,3,+)
>         splice_donor_site(3,3,+)
>         intron(4,6,+)
>         splice_acceptor_site(6,6,+)
>         exon(7,9,+)
>
> HOWEVER, if the gene codes the other way, viz.
>
> 123456789
> EEEIIIEEE
> <<<---<<<
>
> ...we should encode it as:
>         exon(7,9,-)
>         splice_donor_site(6,6,-)
>         intron(4,6,-)
>         splice_acceptor_site(3,3,-)
>         exon(1,3,-)
>
> 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
>
>
>         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
>
>                 --
>                 ______________________________
>
>                 Jannick D. Bendtsen
>                 Senior scientific officer
>
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>
>
>
>         --
>         Lincoln D. Stein
>         Cold Spring Harbor Laboratory
>         1 Bungtown Road
>         Cold Spring Harbor, NY 11724
>         (516) 367-8380 (voice)
>         (516) 367-8389 (fax)
>         FOR URGENT MESSAGES & SCHEDULING,
>         PLEASE CONTACT MY ASSISTANT,
>         SANDRA MICHELSEN, AT mic...@cs...
>
>

-- 
Lincoln D. Stein
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724
(516) 367-8380 (voice)
(516) 367-8389 (fax)
FOR URGENT MESSAGES & SCHEDULING,
PLEASE CONTACT MY ASSISTANT,
SANDRA MICHELSEN, AT mic...@cs...