Re: [EMBOSS] Plasmid drawing
On Sun, 4 Dec 2011 11:25:56 +0100, Stefan wrote: are there any news in plasmid documentation and in-silico cloning with EMBOSS? Pierre Lindenbaum wrote a nice little program called "cloneit" for figuring out cloning strategies. That is, specifically what series of reactions to use to insert a particular piece of DNA into a vector. Not sure if that is what you mean by "in-silico cloning" or not. There is a separate cgi version for web use. Here is the paper: http://www.ncbi.nlm.nih.gov/pubmed/9682060?dopt=Abstract The original distribution site is long since off line, but the code says that it may be redistributed (and incorporated in noncommercial software, but see the exact wording for details.) Anyway, if anybody wants to have a look, I packed up our copies and put them here: http://saf.bio.caltech.edu/pub/software/molbio/cloneit.tar.gz http://saf.bio.caltech.edu/pub/software/molbio/cloneitcgi.tar.gz This is not a graphics program, it is a reaction planning program. As for the graphical output of plasmid diagrams, historically none of the drawing programs does exactly what the end users want. (These get closer and closer, but never quite cover all the bases). For that reason it is really important that the graphics driver be able to output to an object format that can then be imported into a drawing program and edited there. Modifying an image never turns out as nicely. When going to object formats it is key that text remain text and not be converted into line segments or paths. Users get really frustrated when they can't edit labels or change fonts or font sizes. Locally we have a hacked up GCG driver that emits cgm format for the GCG drawing programs. Nowadays going to SVG would make more sense. While it is sometimes possible to read PDF back into a drawing program like inkscape, text imported that way is very hit and miss, mostly miss. Often it comes through with each letter as a separate text object, which is no fun at all to work with. Other times it will come in with each letter separately kerned, and when that kerning is removed, the text jumps all over the place in unpredictable ways. Why would you remove the kerning? Because there is another bug/limitation in inkscape where kerned text is automatically converted to images when exporting to emf or wmf format, as when trying to move that image into a powerpoint document. Moving rotated text between various programs is the most unreliable operation, as far as I can tell. For instance, I have never found a way to get text which runs at an angle other than 0 degrees from inskcape into powerpoint with that angle intact. The text comes through, but the angle is lost. Regards, David Mathog mat...@caltech.edu Manager, Sequence Analysis Facility, Biology Division, Caltech ___ EMBOSS mailing list EMBOSS@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss
Re: [EMBOSS] Plasmid drawing
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 Gesendet von: emboss-boun...@lists.open-bio.org 04/12/2011 21:22 An Stefan Kopie emboss@lists.open-bio.org Thema Re: [EMBOSS] Plasmid drawing On 04/12/2011 10:25, Stefan wrote: 2011/7/7 Peter Rice: 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 _ Marko Hyvonen Department of Biochemistry, University of Cambridge ma...@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 -- ___ EMBOSS mailing list EMBOSS@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss
Re: [EMBOSS] Plasmid drawing
On 05/12/2011 12:52, Hotz, Hans-Rudolf wrote: "cirdna" and "lindna" are nice and do their job most of the time. In my view, the problem is the input file format. Maybe a converter from embl/genbank to *.crip or *.linp would be a good start? Or adding the those formats to the output options of seqret? We do already support "draw" an a report output format. If we add it as a feature output format you can use featcopy (or seqret -feat) to create a cirdna or lindna input file. We can then work on the feature format to add extra information by feature type. We could also add an application to merge a set of feature inputs so you could combine genbank/embl files with restriction map output, then use the results as input. I will see what I can do for the next release. Thanks for the very helpful suggestions Peter Rice EMBOSS Team ___ EMBOSS mailing list EMBOSS@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss
Re: [EMBOSS] Plasmid drawing
> 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. What David wrote is exactly what I wanted to explain with "in-silico cloning". With plasmid documentation I meant that it is possible to draw aplasmid with features and restriction sites. Thanks ___ EMBOSS mailing list EMBOSS@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss
Re: [EMBOSS] Plasmid drawing
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 Gesendet von: emboss-boun...@lists.open-bio.org 04/12/2011 21:22 An Stefan Kopie emboss@lists.open-bio.org Thema Re: [EMBOSS] Plasmid drawing On 04/12/2011 10:25, Stefan wrote: > 2011/7/7 Peter Rice: >> 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
Re: [EMBOSS] Plasmid drawing
On 12/05/2011 10:08 AM, Peter Cock wrote: I use Biopython's GenomeDiagram for this sort of thing, which internally uses a Python library called ReportLab which can produce PDF, SVG, PNG, etc. Sadly I doubt that would be suitable for EMBOSS which would really want a C library. GenomeDiagram has the notion of tracks - which can be useful for separating different types of features which would otherwise overlap (e.g. gene/mRNA/CDS) and other tricks. It also has some defaults about which feature qualifiers to use as the feature name (e.g. gene, locustag). The EMBOSS solution to tracks would probably use the Sequence Ontology to define the tracks, and use features below some specified tag (or set of tags) for each track. We can apply the same tracks to showfeat (the text display of features) Tracks also simplify the issues of colours for features. lindna has code for rendering features withg scaling and avoiding overlaps which we could also, I hope, reuse. Maybe not for the next release (release date 15th January, but code freeze before Christmas) but we can provide applications for testing by anyone interested after the release. regards, Peter Rice EMBOSS Team ___ EMBOSS mailing list EMBOSS@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss
Re: [EMBOSS] Plasmid drawing
On Mon, Dec 5, 2011 at 9:26 AM, Peter Rice wrote: > On 12/05/2011 09:16 AM, Hans-Rudolf Hotz wrote: >> >> Thanks to the Galaxy framework, our lab scientist are using more and >> more EMBOSS tools. Now, it would be very handy if there was an EMBOSS >> drawing tool (even a very simple one) which takes an embl or genbank >> file as input and creates something "colorful". By default each Key or >> Qualifier is given a specific color and shape (eg 'arrow'). And you can >> change them as options. > > Interesting suggestion. Can you send an example of what you > would like to see? > > You can use your favourite drawing tool if you like, but it is OK if > you draw it in crayon, scan it and send the image :-) > I use Biopython's GenomeDiagram for this sort of thing, which internally uses a Python library called ReportLab which can produce PDF, SVG, PNG, etc. Sadly I doubt that would be suitable for EMBOSS which would really want a C library. GenomeDiagram has the notion of tracks - which can be useful for separating different types of features which would otherwise overlap (e.g. gene/mRNA/CDS) and other tricks. It also has some defaults about which feature qualifiers to use as the feature name (e.g. gene, locustag). I have considered writing a Galaxy tool to take an EMBL or GenBank file and produce a picture, but haven't got round to it yet. Anyway, there may be some useful ideas for layout here if nothing else. Peter ___ EMBOSS mailing list EMBOSS@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss
Re: [EMBOSS] Plasmid drawing
On 12/04/2011 09:22 PM, Peter Rice wrote: On 04/12/2011 10:25, Stefan wrote: 2011/7/7 Peter Rice: 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. Hi Peter and Stefan Please allow me to jump in and tell you about our situation: Our wet lab scientist use depending (which lab/university they are coming from) a combination of old commercial products (which we can still use thank to the perpetual licenses) and free/open source products like 'Serial Cloner', 'Ape', 'Gentle', etc I constantly 'preach' how vital it is to make sure you safe each sequence/plasmid/etc not only in the tool specific format, but also in a text format like embl or genbank, where all the annotation is stored in the Feature Table Thanks to the Galaxy framework, our lab scientist are using more and more EMBOSS tools. Now, it would be very handy if there was an EMBOSS drawing tool (even a very simple one) which takes an embl or genbank file as input and creates something "colorful". By default each Key or Qualifier is given a specific color and shape (eg 'arrow'). And you can change them as options. I hope this works as a use case? Regards, Hans Hans-Rudolf Hotz, PhD Bioinformatics Support Friedrich Miescher Institute for Biomedical Research Maulbeerstrasse 66 4058 Basel/Switzerland 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
Re: [EMBOSS] Plasmid drawing
On 12/05/2011 09:16 AM, Hans-Rudolf Hotz wrote: Thanks to the Galaxy framework, our lab scientist are using more and more EMBOSS tools. Now, it would be very handy if there was an EMBOSS drawing tool (even a very simple one) which takes an embl or genbank file as input and creates something "colorful". By default each Key or Qualifier is given a specific color and shape (eg 'arrow'). And you can change them as options. Interesting suggestion. Can you send an example of what you would like to see? You can use your favourite drawing tool if you like, but it is OK if you draw it in crayon, scan it and send the image :-) regards, Peter Rice EMBOSS team ___ EMBOSS mailing list EMBOSS@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss
Re: [EMBOSS] Plasmid drawing
On 04/12/2011 10:25, Stefan wrote: 2011/7/7 Peter Rice: 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
Re: [EMBOSS] Plasmid drawing
2011/7/7 Peter Rice : > Very close to release date next week, so hard to do anything immediately. Hello to the list, 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. I would be happy to hear any progress. Thanks Stefan ___ EMBOSS mailing list EMBOSS@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss
Re: [EMBOSS] Plasmid drawing
On 07/07/11 12:47, Hans-Rudolf Hotz wrote: Hi Peter, We will be happy to help you testing and give feedback, since we are in a very similar situation to Wolfgang. I'm curious. How many sites on this list (as a rough sample) are still running GCG? And how many are using some other commercial package for functions not in EMBOSS? Could be a very useful guide to the new applications needed. Peter ___ EMBOSS mailing list EMBOSS@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss
Re: [EMBOSS] Plasmid drawing
Hi Peter, We will be happy to help you testing and give feedback, since we are in a very similar situation to Wolfgang. Regards, Hans On 07/07/2011 01:33 PM, Peter Rice wrote: Dear Wolfgang, are there any news to plasmid drawing (features and restriction sites) and improvement of cirdna, according to this message from 2005? http://www.mail-archive.com/emboss@emboss.open-bio.org/msg00040.html In our labs this is also a big point for users not to switch completely to emboss. Very close to release date next week, so hard to do anything immediately. However, we did try adding a report format (an output choice for restrict and other applications) to create an input file for cirdna or lindna. Results at the time were poor, but I note we have revised both cirdna and lindna since. I will test whether results have improved. One possibility would be to re-enable this format so you can test and give us feedback on the new release. regards, Peter ___ 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
Re: [EMBOSS] Plasmid drawing
Dear Wolfgang, are there any news to plasmid drawing (features and restriction sites) and improvement of cirdna, according to this message from 2005? http://www.mail-archive.com/emboss@emboss.open-bio.org/msg00040.html In our labs this is also a big point for users not to switch completely to emboss. Very close to release date next week, so hard to do anything immediately. However, we did try adding a report format (an output choice for restrict and other applications) to create an input file for cirdna or lindna. Results at the time were poor, but I note we have revised both cirdna and lindna since. I will test whether results have improved. One possibility would be to re-enable this format so you can test and give us feedback on the new release. regards, Peter ___ EMBOSS mailing list EMBOSS@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss
