[DAS] dsn

[David James Sherman]

  > They are not intended to define a coordinate system.  Entry points can be 
  > arbitrary "interesting areas" within a reference sequence.

Sorry, my mistake then. For some reason I had thought that entry points 
had to be 1-to-1 with reference sequences, since usually they seem to be.

My question about best practice remains, though: how do people organize
lots of little sequences that don't yet share a coordinate system. Here
is the simplest case we have: two ~ 1kb sequences from the opposite ends
of a ~ 5kb insert (call these STCs).

   DP |<----.....~ 3kb.....---->| TP

I would like to have one entry point for the pair, but since the size of
the unsequenced part in the middle isn't known precisely, I can't invent 
a common coordinate system for the STC pair to which to attach the entry
point. Each sequence defines a little, independant, coordinate system.

Can this be done, or is it beyond the intention of the specification?

Thanks for setting me straight about this.


djs               David J. Sherman          (David.Sherman@LaBRI.FR)
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