[DAS2] DAS/2 weekly meeting notes for 14 Nov 05

[Andrew Dalke]

Going through the back emails to prepare for the conference call in 30 
minutes.

Andreas, replying to Steve's comment:
>> For protein DAS, authority typically defines two diff coord systems:
>> 'pdb resnum, interprot'
>
>> It does not permit automated translation between two coord systems.
>
> unfortunately this is not that easy in protein space. The mapping from 
> the 3D
> protein structure to the protein sequence is not straightforward. 
> Think of
> negative, non-consecutive, and "non-numeric" residue numbers that can 
> appear
> in the 3D structures. Therefore we came up with the "alignment" DAS - 
> document
> that allows to map one object in one coordinate system to another one. 
> it can
> also be used to map one assembly to another.

Regarding the structure mapping, when we visited the PDB in August they
said it's not a problem.  The mmCIF records have the information needed
for the mapping.

I've not looked into this though.

> not only - the DAS clients usually can display a certain "coordinate 
> system" e.g. Ensembl can do
> Chromosomal ones, but if DAS sources are available that speak the 
> "UniProt, Protein Sequence" coordinate
> system, it knows how to project these onto the genome. - an 
> "intelligent DAS client" :-)

I like the use case of "user wants to merge annotations from different 
servers.
As DAS currently doesn't have liftover support, the DAS client needs to 
get
annotations only from servers using the same reference coordinate 
system."

					Andrew
					dalke at dalkescientific.com