[Bioperl-l] trans-spliced genes & gff2 & chado

[Lincoln Stein]

I think this representation is going to break a lot of code that assumes, for 
example, that all components of a + strand feature are on the same strand:

> gene
>   transcript-A
>     exon +
>     exon +
>     exon -
>     exon -
>     protein-A
>   transcript-B
>     exon +
>     exon +
>     protein-B

I like this one better:

> gene
>   ts-transcript-1
>     exon +
>     exon +
>   ts-transcript-2
>     exon -
>     exon -
>   transcript-A
>     ts-transcript-1
>     ts-transcript-2
>     protein-A
>   transcript-B
>     exon +
>     exon +
>     protein-B

This is pointing out a weakness in the current bioperl object model in which 
we have combined the ideas of the parts of a compound object with the 
containment hierarchy.   We'll bump into this again when we have to deal with 
enhancers that are 10 kbp away from the gene they regulate and the question 
of "where is the gene" has no simple answer.

Lincoln

>
> On 21 Jul 2003, Charles Hauser wrote:
> > I am generating gff2 to run GBrowse  and have a trans-spliced gene to
> > represent.  I can write code to deal with this particular instance, but
> > was wondering if there is a generic solution?
> >
> > - is there a 'standard/accepted format' to display trans-spliced genes?
> >
> > - in chado I believe one would generate a feature for each segment -
> > correct?
> >
> >
> > Charles
> >
> >
> >      gene            join(32737..32824,complement(174205..174384),
> >                      complement(69520..71506))
> >                      /gene="psaA"
> >                      /note="trans splicing"
> >      CDS             join(32737..32825,complement(174205..174384),
> >                      complement(69520..71506))
> >
> >
> >
> > while( my $seq = $seqio->next_seq ) {
> >     foreach my $f ( $seq->top_SeqFeatures() ) {
> >
> > <snip>
> >
> >
> > 	$out->write_feature($f);
> >     }
> > }
> >
> >
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>
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-- 
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Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein at cshl.org			                  Cold Spring Harbor, NY
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