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

[Charles Hauser]

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);
    }
}