[Bioperl-l] Rfam/Pfam annotations and SimpleAlign

Chris Fields cjfields at uiuc.edu
Fri Oct 27 16:38:17 EDT 2006


Hilmar Lapp wrote:
> You could make SimpleAlign be a Bio::AnnotationHolderI. (I
> suppose this is what you meant by the 'various Bio::Seq Annotation
> methods' too.)
> 
> Just to make sure I'm not misunderstanding, I suppose the
> annotation pertains to the entire alignment?
> 
> 	-hilmar
...

Yes, that's correct.  I would probably use Bio::Seq::Meta for the
sequence-specific markup lines.  I would have to add another new method to
deal with non-sequence-based consensus data (like sec. structure) for now.

Christopher Fields
Postdoctoral Researcher - Switzer Lab
Dept. of Biochemistry
University of Illinois Urbana-Champaign




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