Re: [GUSDEV] additional (AA/NA) sequence attributes

[Chris S. <sto...@pc...>]

Hi Aaron,
Don't think that you got an answer to this so here's my perspective.  
The canonically correct strongly-typed place would be to create a  
view of NASequence / AASequence that has the desired attributes for a  
specific purpose (and the view would be named as such). On the other  
hand if these are overlooked attributes that really should be part of  
any sequence then we would alter the base NASequence/ AASequence  
tables. The major argument I would see for weak typed tag values is  
that there is a long and arbitrary list of such attributes but I'm  
not convinced that this is the case.

Are the examples you gave, attributes needed now? Are there others?
Thanks,
Chris

On Nov 17, 2005, at 10:01 PM, am...@pc... wrote:

>
> Where is the "canonically correct" place to store simple scalar  
> attributes that
> pertain to an entire sequence (AA and/or NT), e.g.:
>
>   pI (isoelectric point)
>   codon volatility
>   codon bias (measured in various ways: CAI, etc)
>   dinucleotide bias (e.g. Karlin's delta*)
>
> My non-GUS "gut" instinct is that these should all reside in weakly- 
> typed
> DoTS.(NA/AA)SequenceAttribute tables with very simple tag/value  
> schemas; but
> I'm looking for enlightenment.
>
> Thanks,
>
> -Aaron
>
>
>
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