[Bioperl-l] Huh? Bioperl Seq objects and strands

David Block dblock@gene.pbi.nrc.ca
Fri, 15 Sep 2000 12:06:03 -0600 (CST)

Hi experienced bioperlers,

We're trying to map a Bio::SeqI compliant object onto a Tk Map.  We're
very close (code within days for this part), but we're fighting with the
Seq object's definitions of gene, exon, and CDS.

We loaded up a Bio::Seq object from GenBank using SeqIO.  Top-level
features for genes on the -1 strand have the tags
gene  strand 1
gene_span strand 0
intron strand -1
exon strand -1

How can we tell which top-level features with strand 1 are actually strand
-1 without looking at sub-features?  We would like to be able to decide so
we can map the gene on the correct side of the axis.

Also, why are introns and exons top-level features of a sequence, when
they are also (obviously) sub-features of a gene?

Shouldn't it be (top-level features only):
gene strand -1
gene_span strand 0

and that gene's subfeatures:
intron strand -1
exon strand -1


Dave "Huh?" Block, with commentary by Mark "I Dunno???" Wilkinson