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 _______________________________________________ EMBOSS mailing list EMBOSS@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss _______________________________________________ EMBOSS mailing list EMBOSS@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss