[Pipet Devel] [Fwd: Development]

[J.W. Bizzaro]

Thomas.Sicheritz at molbio.uu.se wrote:
> 
>  > I can't recall exactly how your Tcl/Tk editor works.  I may have
>  > described much of it already.  I think this is a fun tool to be working
>  > on.
> 
> You can look at a VERY stripped tclet ( Tcl/Tk Applet) version at
> http://evolution.bmc.uu.se/~thomas/loci/xbblet.tcl
> 

Yes it is very much how I described :-)  But the editing locus I was thinking of
would make use of XML to display the context of the sequence...if available. 
That is, a sequence that comes from a GenBank document would _always_ retain
information on where the UTR, CDS, exon and intron, etc. regions are.  So I see
a sequence in the editor displayed as a "genetic map".  You know how molecular
biologists draw out horizontal bars of different colors representing different
regions, binding sites, etc.  I think the editor can show a color-coded map with
ACGT bases transposed over the map or maybe sitting below it.  Looking at
molecular bio journals might help to find an informative and attractive
solution.

I know we don't have the facility right now to go from GenBank to XML to
representation.  This facility might be a good starting point for Justin and
others who are well versed in XML/DOM...hint hint ;-)


Jeff
-- 
J.W. Bizzaro                  Phone: 617-552-3905
Boston College                mailto:bizzaro at bc.edu
Department of Chemistry       http://www.uml.edu/Dept/Chem/Bizzaro/
--