[Bioperl-l] Bio::SeqFeature::Annotated / SOFA question

Sendu Bala bix at sendu.me.uk
Thu Sep 27 09:47:06 EDT 2007


I want to create a Bio::SeqFeature::Annotated object where the 'type' is 
'conserved_region'.

I got the idea that 'conserved_region' might be ok from here:
http://song.sourceforge.net/SOterm_tables.html#SO:0000330

However, this doesn't work since:

------------- EXCEPTION -------------
MSG: couldn't find a SOFA term matching type 'conserved_region'.
STACK Bio::SeqFeature::Annotated::type 
/data/bioinf/home/sb/current/bioperl-core/Bio/SeqFeature/Annotated.pm:371
[snip]


I'm guessing Bio::Ontology::OntologyStore is getting its allowed SOFA 
terms from:
http://umn.dl.sourceforge.net/sourceforge/song/sofa.definition


I don't know much about this area. Can someone offer a little guidance 
as to what the significance of these two different files is, why they 
don't contain the same terms, and why I can't use 'conserved_region'?

What's the closest alternative term?


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