Going from EMBL annotations to ACE - sequence objects...

Mark Wilkinson markw at cheerful.com
Mon Jan 17 10:20:22 EST 2000


Dear Ace'ers,

My 'community' is in the habit of submitting to EMBL just the genomic
sequence of a given gene, nicely annotated with introns and exons and
such.... but not always submitting the corresponding cDNA sequence.

had presumed that you would be able to simply tell ACE which parts of
the genomic sequence object corresponded to exons and which corresponded
to introns (in much the same way as it is able to assign other EMBL
features to regions) but this doesn't appear to be the case.

I want to generate these "pretty pictures" where the exon/intron
structure is overlayed on the sequence, but it appears that this can
only be done when the db contains both the genomic *and* the cDNA
sequence objects, and strangely this information is contained in the
cDNA sequence object rather than the genomic sequence object!  This
seems counter-intuitive to me... intron/exon information is in genomic
DNA not in cDNA!!

Can someone explain the logic to me? and isn't it a bit redundant to
have both sequence objects when a genomic with annotations does the same
thing?

Cheers all!
Mark







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