[DAS2] transitioning from DAS/1 to DAS/2

[Steve Chervitz]

Andreas Prlic wrote:
> Hi Andrew!
> ...
>>   - DAS/2 genomic annotations
>>   - DAS/2 protein annotations
>>   - DAS/2 structure
> 
> this are the DAS2 - "domains" This leads to a discussion I would like
> to have next monday:
> 
> DAS1 is rather powerful, because it is possible to use the sequence and
> features commands
> in a way that works for both genomic and protein sequences.  There is
> no need to distinguish between these
> in the DAS1 - world.
> 
> I understand that one of the reason for creating the DAS2-"domains" is
> to have several "modules"  which can be
> extended/developed independently. Still the genome -domain is very
> similar to what is needed for any kind of
> sequence.
> 
> I would therefore like to discuss to rename the "genome" domain to
> "sequence".
> 
> The information of which type of sequence, "genomic" or "protein
> sequence"  should be provided via the
> source description.

I like this idea. The only nucleotide specific stuff in the DAS/2 retrieval
spec is the region request. Strand designation in a location specifier is
already optional.

We'd may then want to change the 'sequence' request to something else,
perhaps 'residues'?

Steve