[EMBOSS] Plasmid drawing

[Hans-Rudolf Hotz]

On 12/04/2011 09:22 PM, Peter Rice wrote:
> 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.
>

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
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