Plasmid draw program for IBM

J Preiss--Seq Anal preissj at CLVAX1.CL.MSU.EDU
Tue Jan 5 23:41:00 EST 1993


Plasmid.drw

I have a request to post to the bio software net.  I want a
program to draw plasmids for IBM/DOS based computers.  I have
compiled a wish list of what I want in such a program.  If anyone
knows of any program that comes close to my desires, I would
appreciate hearing about it.  Also, if any programmers monitor
this net, I would like to see such a program written.  I have
heard of several programs for the Mac which are supposed to come
close, but none that really does the job.  I am also aware of
Clone, plus Enhance from Scientific & Educational Software for
IBM.  It is a very nice program, from what I've heard, but a
little out of my price range at $650- last I checked.
     I would invite others to comment on my wish list, add to it,
direct me to their favorite program, or tell me that I am a fool
for asking for so much for so little.  With any luck, I will
either find what I'm looking for, or inspire some enterprising
programmer to write it.

Things I want in a plasmid drawing program for IBM computers.

1.   Low cost, around $250-
     Based on informal surveys of my colleagues, my estimates for
how many copies you could sell, worldwide, of a good program are
as follows:          $250-         10,000
                     $500-          1,000
                    $1000-            100    Ok, very informal.

2.   Ability to take in data and output data in formats that are
easily compatible with other systems and programs.
     Most computer users have more than one program loaded on
their hard drive, and we each have our favorite for doing certain
functions.  My favorite programs are those that allow me to do
what that program does best and transfer to another program for
other functions.  An example, I entered my sequence on a
digitizer with Microgene, edited it with MS Word, performed
sequence analysis on GCG, prepared it for publication on Aldus
Pagemaker and prepared slides to present it at meetings with
Powerpoint.

3.   Ability to take input as either sequence (in ASCII files) or
as point info (eg, this site here, that gene there, on a plasmid
this big).

4.   Ability to produce publication quality plasmid and clone
drawings.  Printed graphics must be clear and sharp and
comparable in print quality with those drawn by graphic artists
and published in existing literature.

5.   Ability to accommodate new genetic elements and features.  

     Different scientists want to highlight different things in
their published plasmid diagrams.  Some elements are point sites,
some cover a region.  Some are directional, some not.  Some
elements are embedded within other other features.  Others are
fragments eg, the 5' region of a gene, and may be linked to
another fragment, eg the 3' region of another gene.  Some
features are too detailed to be shown directly in the diagram and
need to be blown up, eg, a multiple cloning site.

6.   Modifiable or editable final picture.  I sometimes want to
modify things to highlight features I am discussing in the text
or minimize things like mundane vector functions.  Can I have the
final say in how the figure looks please?

7.   Many options for shading and fill patterns in black and
white laser prints.  Most of the scientific community publishes
in black and white.  Color options are nice for seminars, but we
need black and white to publish.

8.   Ability to combine several plasmid and clone drawings on a
single page with other graphics.  This may really be part of my
request to have file formats that can be accessed in many
programs.  If I could paste several clone diagrams into a file in
another program and draw arrows and text between to make flow
diagrams showing the history of construction of a plasmid, that
would be perfect.

9.   Identify all known restriction enzyme sites and names.  I
would like the program to identify, and include in the final
diagram, all sites that I ask it to.  An extension of this is to
have it include all unique cutting enzymes, or all enzymes that
cut less than 3 times or more than 10 times, or what ever I
choose that day.  A useful, but not necessary, side function here
would be the ability to provide a list of restriction fragments
resulting from any single or multiple digest and sizes of
fragments in order of size.

10.  Simple cloning functions to allow creation of new plasmids
from pieces of existing figures.  Nothing fancy is required here,
but it should be able to cut at specified restriction enzyme
sites, modify ends with typical enzymes (eg, Klenow, T4-Pol...)
and ligate, while maintaining the correct resultant sequence.


          Thanks

          Dr.  Leonard N. Bloksberg
          PreissJ at clvax1.cl.msu.edu
          Dept. of Biochemistry
          Michigan State University

                         "Life is weird"






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