Plasmid drawing software

Mathew Woodwark mathew.woodwark at bbsrc.ac.uk
Wed Jul 5 04:27:10 EST 1995


Massimo Delledonne <delledonne at sc2.salk.edu> wrote:
>>pgegen at DawnTreader.bio.ukans.edu  (Peter Gegenheimer) wrote:
>>
>>>WHY DO PEOPLE WANT SUPERB, FEATURE-RICH SOFTWARE BUT DON'T EXPECT TO PAY FOR 
>>>IT??? 
>>
>
>Ok, that's a good question ..... Money problem I think ....
>But there are several things programmers should consider ....
>There are several good shareware programs out there  in any field ....
>I don't think I need to remind you how many megabites of windows or mac 
>or unix or dos programs people wrote, and also for molecular biology I 
>can use several good FREE or shareware programs that help me in my work 
>.. What I don't have yet is a simple program that help me drawing 
>plasmids for presentation or pubblications ... I'm not looking for a big 
>program that allow me to handle ANY kind of sequence or piece of DNA or 
>protein and so on ... I already pay an annual fee to use GCG and that's 
>enough for my budget .... I think a lot of people out there is not 
>looking for a program that draw a plasmid from a sequence (using may 
>be one of those (in my opinion) TERRIBLE programs that require a key in 
>the parallel port to works, making impossible keep a copy of the program 
>in my notebook. ( I pay for GCG, but I can connect to my GCG from 
>everywhere in the world via internet, I'm not forced to use it only from 
>the computer I have in the lab)
>So far I'm using HG for Windows, but I have to draw a circle, draw some 
>arcs and so on ... pretty painfull but I don't have anything else .....
>
>I don't think big groups like NCBI or EMBL or some computing groups 
>wouldn't be able of give us a so simple program .....
>
>
If you have a license for GCG, why not use PLASMIDMAP. I know its not the 
prettiest graphics in the world, but it does the job. If you run mapsort/plasmid, 
you can edit the resultant tick file like so:

Original:

Name           From   To       Strand    Color Fromsymbol Tosymbol Style ..

eco0109I       392    392        .       green      .       .     tick
eco0190I       513    513        .       green      .       .     tick
haeI           844    844        .       black      .       .     tick
haeI           972    972        .       black      .       .     tick
hin41          536    536        .       black      .       .     tick
hin41          722    722        .       black      .       .     tick

edited:

eco0190I       392    513        -       green      >       >     range
haeI           844    972        +       black      |       >     range
hin41          536    722        +       black      .       .     block

(stuff deleted)

This gives you an output in blocks and ranges and restriction sites of enzymes for 
your plasmid. I know its not windows, but it does the job.


>=========================================================================
>=========
>Massimo Delledonne, PhD
>
>permanent address: Istituto di Genetica Vegetale
>                   Universita' Cattolica S.Cuore, 29100 Piacenza ITALY
>                   Ph. (+39) 523-599209    Fax (+39) 523-599283
>                   internet: delle at pc.unicatt.it   
>
(more stuff deleted so I can post this message)

Cheers

Mathew

-- 
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Dr Mathew Woodwark		            mathew.woodwark at bbsrc.ac.uk
Molecular Biology Software Support          Tel: 01582 762271
BBSRC Computing Centre                      Fax: 01582 761710
West Common, Harpenden
Hertfordshire, AL5 2JE, UK
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