Annotating sequence for publication

lonetto at CGL.UCSF.EDU lonetto at CGL.UCSF.EDU
Wed Jul 17 15:06:32 EST 1996


I've been using "prettybox" on our unix machine running GCG.  It
uses the GCG shared libraries and such, so you really need GCG
for it to be useful.  It works very similar to "pretty" and is
quite flexible with regard to output shading, etc, though there
is no easy way of boxing or shading specific segments/residues.

Output is postscript which Adobe Illustrator 6.0 r greater can
interpret (nice for annotating/making finished figures).  I 
usually use illustrator to convert to EPS with a preview and
place the EPS file into another illustrator file to make the
final figure (performance is much better).  Note on bugs:  
the version of prettybox we're using has a bug/bad feature 
when used for postscript output:  It dumps the entire output
into a single file.  Since EPS is a single page format, if 
you output a multipage document only the last page prints/converts.

I get around this by only sending one page of output at a time, or
by editting the postscript output into separate files for each page
of output (not for the squeamish, make sure you duplicate the header 
in each file!).  I've been running prettybox on a DEC alpha (unix) and 
Illustrator on a Powermac.  The illustrator part should work on 
a PC as well, but you'll need either a powermac or a Pentium machine with 
LOTS of RAM to do it without severe frustration.

Disclaimer:  I don't work for adobe and gain nothing by endorsing
Prettybox (if you can call this an endorsement:-).  Though of course,
if Adobe wants to start sending me free software I'd be happy to
change my disclaimer :-)

-=-=-=-=-=-=-            Mike Lonetto                   lonetto at
UCSF Dept of Stomatology, 513 Parnassus Avenue, San Francisco, CA 94143-0512
	Subject: Annotating sequence for publication
	Date: 16 Jul 1996 13:47:33 GMT
	Message-ID: <4sg6hl$g82 at>
	What software are you using for the purpose of creating figures that
	display sequence with annotation, such as text and highlighting?
	What I would find most useful would be Mac or Unix-based software that
	outputs graphics in a few of the most popular formats, e.g. 
	of interest.
	JD_Tisdall at 
	James D. Tisdall
	Manager, Computational Biology Group	Phone: (215) 728-3660
	The Fox Chase Cancer Center		FAX:   (215) 728-2513

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