Plasmid drawing software
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
>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:
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
eco0190I 392 513 - green > > range
haeI 844 972 + black | > range
hin41 536 722 + black . . block
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)
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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