Annotating sequence for publication

[Geoff Barton]

James D. Tisdall wrote:
> 
> 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.
> encapsulated color postscript.  But any solution you use would be
> of interest.

You could try ALSCRIPT.  This takes an alignment and produces
PostScript.  It is pretty flexible, but takes a little learning.
see ftp://geoff.biop.ox.ac.uk/README for download instructions.
see http://geoff.biop.ox.ac.uk/manuals/alscript/alscript.html for the
on-line manual.  See 
http://geoff.biop.ox.ac.uk/papers/alscript/alps2.html for an
on-line  preprint of the paper published in Prot. Eng. in 1993.

You may also like to try the AMAS server on the WWW.  AMAS allows a 
multiple alignment to be analysed for "interesting" conservation 
patterns - one output is a PostScript file that boxes and shades the
alignment.

See:
http://geoff.biop.ox.ac.uk/servers/amas_server.html. 

Geoff.


-- 
Geoffrey J. Barton, Laboratory of Molecular Biophysics, University of
Oxford, 
Rex Richards Building, South Parks Road, Oxford OX1 3QU, U.K.
mailto:gjb at bioch.ox.ac.uk, Tel: +44 1865 275368, Fax: +44 1865 510454, 
ftp://geoff.biop.ox.ac.uk, http://geoff.biop.ox.ac.uk