PlasmidDrawing for Mac?

Keith James kdj at fes6.sanger.ac.uk
Mon Apr 26 03:57:21 EST 1999


>>>>> "Cornelius" == Cornelius Krasel <krasel at wpxx02.toxi.uni-wuerzburg.de
    > writes:

    Cornelius> Harry Mangalam <mangalam at home.com> wrote:
    >> What would you like to see for plasmid drawing? (Or anything
    >> else for that matter..)
[..]
    Cornelius> 1) A map compiler. This program would take a textfile
    Cornelius> in some kind of format (e.g. GCG plasmidmap format) and
    Cornelius> generate a map out of it (preferable output format is
    Cornelius> something object-oriented, e.g. postscript, xfig or
    Cornelius> similar, since this allows manipulation of the
    Cornelius> generated format with something else. Output in a pixel
    Cornelius> kind of format can be generated out of postscript with
    Cornelius> ghostscript without any problems.)

There is something a little like this which will generate a linear map 
in 6 frames, although it's not quite what you describe. It's a Java 
annotation tool developed at the Sanger Centre and freely distributed 
(see www.sanger.ac.uk/Software/Artemis/index.shtml). We use it as our 
main annotation tool. Any features can be added in EMBL feature table 
format. The output of Fasta/Blast/Gap/RE searches are parsed into EMBL 
with Perl scripts and overlaid. As yet you have to get printed output 
by grabbing screen dumps, so like I said, not quite what you described.

    Cornelius> 2) A graphical program (kinda xfig-like) which allows
    Cornelius> construction of plasmids by mouse-clicking. This
    Cornelius> program would produce either the textfile mentioned
    Cornelius> under (1) or the object-oriented graphics output.  It
    Cornelius> should be able to read the textfile as well and display
    Cornelius> it on-screen.  I wonder if one could build something
    Cornelius> like that with Tk.

I was planning on using Perl/Tk with the BioPerl modules and EMBL.pm 
for parsing EMBL entries obtained by efetch. The features could be 
rendered on a Tk canvas which gives PostScript dumps without having 
to generate PostScript directly. The Bioperl restriction cutting module 
isn't fully developed as yet, so I was considering parsing tacg output.

    Cornelius> 3) It would be nice to have a program which could
    Cornelius> convert sequence information directly into the text
    Cornelius> format mentioned under (1). I think tacg might be up to
    Cornelius> that task. It would be even nicer if the program could
    Cornelius> find some commonly used genes (like ampR in a plasmid)
    Cornelius> by itself, either by doing some kind of sequence
    Cornelius> comparison or by parsing genebank headers.

If you use the Perl, EMBL.pm already does this. It's a nice idea. Also 
the ability to include DNA for which no sequence data is available so 
that plasmid diagrams could still be drawn when uncharacterised 
fragments have been cloned would be important for some lab workers.

If I come up with anything useful I'd be happy to offer it to anyone 
working on an open source plasmid tool (it's early days, though).

-- 

Keith James  --  kdj at sanger.ac.uk  --  http://www.sanger.ac.uk/Users/kdj
The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SA




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