Re: [Treebase-devel] [CDAO-discuss] lat/lon in nexml

[Arlin S. <sto...@um...>]

On Feb 12, 2010, at 9:38 AM, Hilmar Lapp wrote:

> CDAOers: what are status and plans for describing the parts of an
> alignment right now, and is there support, current or planned, for
> partitions / segments of an alignment?

Right now there is not even a fully worked out concept of sequence,  
only states of characters.  So, in the matrix:

OTU1 TCAAG
OTU2 TAAAG

there is no "sequence" concept telling us that "T" and "C" in OTU1 are  
sequentially ordered residues.    They are treated just like classical  
character states in that sense.

One way to deal with this is via MAO, the multiple alignment  
ontology.  We developed a mapping between MAO and CDAO last summer  
that might be useful for this.  MAO has a concept of sub-alignments  
that might be useful here.

Also, in CDAO there is a "coordinate system" concept that we intended  
to use to impose a mapping on characters in a sequence.  The concept  
has not been fleshed out yet.

If there is a coordinate system CS1, with "T" and "C" assigned  
coordinates "1" and "2", and another coordinate system CS2 with "A",  
"A", and "G" assigned coordinates "1", "2" and "3", then this would be  
a way to represent that the data from OTU1 come from 2 different  
sequences.

Arlin