Sequence boxing programs

Roy Smith roy at phri.nyu.edu
Tue Apr 2 11:16:14 EST 1991

Kay Hofmann <budi at genetik.uni-koeln.de> writes:
> I myself have written a quick&dirty program in VAX-Pascal that takes
> PRETTY-output files from GCG-LINEUP (CLUSTAL files to come soon) and
> shades them in colors or gray-scales according to identity or amino acid
> similarity.

	I have a similar sort of program I call homochart which takes an
ascii file containing a bunch of aligned sequences and generates PostScript
directly to make a nicely shaded homology chart (hence the name).  It's
written in C (originally under SunOS-3.5.2; I don't know of any reason it
shouldn't port to other environments, but I havn't actually tried).  For an
example of what the output looks like, look at Figure 6 in Weinrauch et al,
J. Bacteriol. 171, pp 5362-5375 (1989).  Actually, I just went to look it
up in the library and discovered that that particular example reproduced
terribly in the journal; I think they were sent a 300 dpi LaserWriter
original instead of a 2540 dpi Lino print, and I suspect the printers shot
it badly on top of that.  When done on the Lino and printed well, they
really do look good.

	Homochart is a bit of a hack, so it has some rough edges, but
people are free to make whatever use of it they like.  You can get it via
anonymous ftp from goober.phri.nyu.edu ( in the /pub/seq
directory.  You want to get the file homochart.tar, making sure to use
binary mode when you download it.  I regret that I don't have the time to
honor requests to distribute the program other than by anonymous ftp.  I
know some other folks maintain mail servers for software like this; if they
could get the tar file and add it to their servers, I would appreciate it.
Roy Smith, Public Health Research Institute
455 First Avenue, New York, NY 10016
roy at alanine.phri.nyu.edu -OR- {att,cmcl2,rutgers,hombre}!phri!roy
"Arcane?  Did you say arcane?  It wouldn't be Unix if it wasn't arcane!"

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