[Bioperl-l] Bio::Species/Bio::Taxonomy changes

[Hilmar Lapp]

On Jul 24, 2006, at 8:34 AM, Sendu Bala wrote:

> Hilmar Lapp wrote:
>>
>> On Jul 24, 2006, at 3:58 AM, Sendu Bala wrote:
>>
>>> On a side note, why would we care about 'organelle' when we're  
>>> dealing
>>> with taxonomy? Why does the NCBI taxonomy db have a slot for  
>>> organelle?
>> Because some sequences are of the organelle DNA, and Genbank needs  
>> a way
>> to express this. Highly artificial, but still can't be ignored.
>
> Ok, but why is it stored as part of the taxonomy? Why isn't it  
> stored in
> its own field? And does /bioperl/ have to store it as part of the
> taxonomy?

No, but clients need to be able to obtain it. Organelles have their  
own genome. If we talk about the human genome, for instance, most  
commonly we refer to the nuclear genome only.

> Maybe the file parser could have its own organelle() method
> and leave all taxonomic classes without such a method. Or it could  
> stay
> as is, I don't know.

Like I said above, at the end of the day there needs to be a way to  
qualify a sequence by the genome it is part of.

>
> Do different organelles in the same species get unique taxonomy ids?

I would have to confirm, but I believe so. As I said, from a genome/ 
sequence-centric viewpoint, the organelle and nuclear genomes are two  
different things.

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