[Bioperl-l] Re: [Gmod-gbrowse] trans-spliced genes & gff2 & chado

[Lincoln Stein]

Cool.  Unfortunately there isn't generic code for trans-splicing that I know 
of.  I've been thinking of generating a little glyph that will show a short 
leader "hanging off" the first exon.

Lincoln

On Monday 21 July 2003 09:01 am, 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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-- 
========================================================================
Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein at cshl.org			                  Cold Spring Harbor, NY
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