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.ba...@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 <p...@ebi.ac.uk>
Gesendet von: emboss-boun...@lists.open-bio.org
04/12/2011 21:22
An
Stefan <s.newsli...@gmail.com>
Kopie
emboss@lists.open-bio.org
Thema
Re: [EMBOSS] Plasmid drawing
On 04/12/2011 10:25, Stefan wrote:
2011/7/7 Peter Rice<p...@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
ma...@cryst.bioc.cam.ac.uk
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