[EMBOSS] Plasmid drawing

[Marko Hyvonen]

I would find this kind of in silico cloning great addition to EMBOSS.

As an example of (a free?) drawing program for plasmids, I use PlasMapper 
(http://wishart.biology.ualberta.ca/PlasMapper/ , source code is at least 
available on the site). Here is an example I made from their own selection 
of plasmids (hopefully valid link for a while still):
  http://wishart.biology.ualberta.ca/PlasMapper/jsp/displayPlasmidMap.jsp?fileName=plasMap26_1323082022185.png&fileFormat=png

I like the fact that it includes a number of predefined features in 
plasmids as built-ins, so that you only need to include the "unique" 
features in your own plasmids (and I am sure the set of built-ins could be 
expanded much further). Outputs svg too, which is brilliant for editing 
later on.

Marko


On Mon, 5 Dec 2011, david.bauer at bayer.com wrote:

> Hi Peter,
>
> I think Stefan means not only the drawing of plasmid maps but the creation
> of new constructs in the computer before doing it at the bench.
> This is a field where there are currently only commercial packages
> available like VectorNTI and Clone Manager (
> http://www.scied.com/pr_cmpro.htm) etc.
> Clone manager is there since the times of MS-DOS but the prices have
> increased substantially. They used to advertise the software with the
> slogan: "It costs only as much as a cloning kit for the lab" - which was
> in the range of 300,-USD.
>
> The most important functions, which I think should be implement first are
> the cloning operations.
> So e.g.
> - take plasmid1, open the multi cloning site with BamHI and EcoRI
> - take plasmid2, cut out a fragment with BglII and EcoRI
> - ligate the fragment from plasmid2 into plasmid1
>        (BamHI and BglII have compatible ends which can be ligated, so an
> algorithm is needed to check this)
> - draw a map of the newly created plasmid3
> This is a rather simple example.
> There can be more complex procedures like Klenow fill in (blunt end
> ligation of incompatible restriction sites) or the use of more than 2
> fragments in one ligation.
>
> I think most of the functions needed for this are already present in
> EMBOSS.
> It shouldn't be so complicated to create an application which uses
> functions from restrict, cutseq, pasteseq to accomplish the above
> mentioned task.
> Although it's probably not so trivial to make this happen before the
> release next week ;-)
>
> Cheers,
> David.
>
>
>
>
> Peter Rice <pmr at ebi.ac.uk>
> Gesendet von: emboss-bounces at lists.open-bio.org
> 04/12/2011 21:22
>
> An
> Stefan <s.newslists at gmail.com>
> Kopie
> emboss at lists.open-bio.org
> Thema
> Re: [EMBOSS] Plasmid drawing
>
>
>
>
>
>
> On 04/12/2011 10:25, Stefan wrote:
>> 2011/7/7 Peter Rice<pmr at ebi.ac.uk>:
>>> Very close to release date next week, so hard to do anything
> immediately.
>>
>> are there any news in plasmid documentation and in-silico cloning with
>> EMBOSS? In the last month I was asked 4 times if this is possible with
>> EMBOSS. People like it to work with EMBOSS and want to do that things
>> also with this suite.
>
> Can you give us some examples of what you would like to see? Examples
> always help us to design new applicatons.
>
> We still only have cirdna, mainly because we are limited by the plplot
> graphics library (and would welcome suggestions of other graphics
> libraries we could try).
>
> We have extended the capabilities by creating input files from some
> other applications.
>
> regards,
>
> Peter Rice
> EMBOSS team
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  _____________________________________

  Marko Hyvonen
  Department of Biochemistry, University of Cambridge
  marko at cryst.bioc.cam.ac.uk
  http://www-cryst.bioc.cam.ac.uk/groups/hyvonen
  tel:    +44-(0)1223-766 044
  mobile: +44-(0)7796-174 877
  fax:    +44-(0)1223-766 002
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