[Bioperl-l] Bio::LocatableSeq and Annotation vs Feature

Chase Miller chmille4 at gmail.com
Thu Jun 25 10:46:26 EDT 2009


Hi all,

Quick question I came across while writing the Bio::Nexml module.

I'm trying to link taxon data to a Bio::LocatableSeq object inside a
Bio::SimpleAlign object.  Bio::SimpleAlign has the ability to add
SeqFeatures, but according to this HowTo (
http://www.bioperl.org/wiki/HOWTO:Feature-Annotation) a feature is
considered to refer to a portion of a sequence, whereas something like taxon
data would refer to the entire sequence and should be handled as an
annotation. However, as far as I can tell Bio::LocatableSeq does not support
annotation objects.
What would be the best way to relate taxon data to a single sequence inside
an alignment?


Thanks,
Chase


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