roy@phri.nyu.edu (Roy Smith) (04/05/91)
Archive-name: bionet/sequences/homochart/1991-04-02 Archive: goober.phri.nyu.edu:/pub/seq/homochart.tar [128.122.136.10] Original-posting-by: roy@phri.nyu.edu (Roy Smith) Original-subject: Re: Sequence boxing programs Reposted-by: emv@msen.com (Edward Vielmetti, MSEN) Kay Hofmann <budi@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 (128.122.136.10) 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@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!"