[DAS] "inter-base" location format

[Brian King]

Lincoln,

I'm interested in the "inter-base" method of
specifying locations that you mentioned here and in
the bioperl forum.  Is there any documentation on how
it's done and its merits?  I'm giving a presentation
on genomic XML at the I3C meeting next week.  I'll be
talking about location representation requirements,
since a common location format is a high priority for
data exchange.  I'm also always looking for ways to
improve AGAVE XML.  I appreciate any information you
can give me.

Regards,
Brian  



>> * Does a server have to deal in 1-based sequence
coordinates to be
 > DAS1-compliant? I'm assuming yes, but it would be
good to state so 
explicitly
 > in the spec. This is relevant to a recent thread on
the Bioperl 
list: 
 > 
 >
http://bioperl.org/pipermail/bioperl-l/2002-July/008318.html
 > 
 > Internally, we make much use of 0-based half-open
intervals (or 
"inter-base"
 > coordinates as we call them, where the numbers
refer to the 
positions
 > in-between the bases). It would be great if a
server could specify 
the
 > coordinate system it uses. It would then be up to
the client to do 
the
 > appropriate conversion if necessary. Perhaps
something for DAS2?

You are right that 1-based closed intervals are used. 
Possibly this
is something that could be made optional in DAS2, but
I would prefer
to pick a single coordinate system convention and
stick to it.
I agree that Interbase coordinates are better than the
current
convention in Bioperl and elsewhere.

Lincoln




__________________________________________________
Do You Yahoo!?
Yahoo! Health - Feel better, live better
http://health.yahoo.com