[Bioperl-l] Phyloxml SeqI without actual sequence

Hilmar Lapp hlapp at gmx.net
Tue Jul 29 13:59:24 EDT 2008


On Jul 29, 2008, at 1:31 PM, miraceti wrote:

> sometimes the clade looks like.
>
>               <sequence>
>                  <annotation>
>                     <desc>alcohol dehydrogenase</desc>
>                     <confidence type="probability">0.99</confidence>
>                  </annotation>
>               </sequence>
>
> sometimes the clade looks like.
>
>                 <sequence>
>                  <symbol>ADHX</symbol>
>                  <accession source="UniProtKB">P81431</accession>
>                  <name>Alcohol dehydrogenase class-3</name>
>
> <mol_seq>TDATGKPIKCMAAIAWEAKKPLSIEEVEVAPPKSGEVRIKILHSGVCHTD</mol_seq>
>                  <annotation ref="EC:1.1.1.1"/>
>                  <annotation ref="GO:0004022"/>
>               </sequence>
>
> Do you think it's better not to create the SeqI in the first case?.

It's an option but to me it threatens to lose the fact that the  
annotation properties pertain to a sequence, not to something else  
(such as the tree node, for example). So, if you don't attach the  
annotation to a sequence object you create, what would you attach it  
to then? In the absence of a good answer creating the sequence object  
may the only way.

I thought I'd recall some kind of Bio::Seq::EmptySeq object for  
exactly this kind of case, but apparently there isn't one there, so  
maybe I was just dreaming this up. However, a sequence object that is  
optimized for this case may be useful to have, though thinking about  
it, I'm not exactly sure what overhead the sequence slot really adds  
to all the other overhead added by feature and annotation slots. The  
only thing that really comes to mind is that a sequence object with a  
zero length sequence won't allow you to add features.

Sorry for this random stream of thoughts here, I hope I'm not totally  
wasting everyone's time here.

	-hilmar
-- 
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: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
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