[EMBOSS] Plasmid drawing

[mathog]

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
mathog at caltech.edu
Manager, Sequence Analysis Facility, Biology Division, Caltech