Hi Leyla - This is a really good question 
I need to know if there is a key of colours and shapes for the graphical
representation of annotations in proteins. for instance, if I need to
have a pictorial representation of a "domain" or "transcript" then is
there a standardized way to do it? So far I have seen that domains are
usually represented as ellipses or rectangles, and metal bindings as
non-filled circles, while active sites are red-filled circles.
I am particular interested in the next type of annotations:
Domain, Signal, Transit, Propeptide, Peptide, Topological domain,
Intramembrane, Transmenbrane for ranges of sequences, and Metal binding,
Active site, Modified residue, Lipidation, Glycosilation for point
positions.
I don't know of any single widely accepted notation for this kind of
annotation, only of the conventions defined by certain programs and
websites.
Off the top of my head, however (deep breath) ... Single position
annotation conventions for proteins have mostly been developed by the
structural community for marking up sequences (e.g. LigPlot, PDBsum,
etc) but several have come from sequence databases like uniprot. Domains
are far more varied - and I think there are at least a couple of schools
here (CDART, SMART and Interpro/Pfam) - in particular, colours tend to
be used to distinguish different domains in a diagram, rather than to
attribute the exact type of domain. I doubt there is any real standard
for PTM/chemically modified residues - except for certain types of
amidoglycans (often, here, the important aspect is to distinguish mono,
bi and triantennary sugar chains, with or without phosphoglycan). In the
genome community, I'm sure that the standards are again stemming from
the types of databases/tools people use (ensembl vs Entrez vs Apollo vs
UCSC Genome Browser), as well as the kind of information relevant for a
particular organism (e.g. bacterial/plant/animal type genome
architecture). I could go on with this ramble - but instead, I'd love to
hear if any one else knows of any accepted standards !
Jim.
ps. Leyla - I'll be at the DAS developer's meeting this thursday and
Friday if you are interested in talking about this in person.
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On 28/02/2011 13:13, Leyla Garcia wrote: