[EMBOSS] Plasmid drawing

[david.bauer at bayer.com]

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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