budi@GEN1.GENETIK.UNI-KOELN.DE (03/28/91)
Hello! Sure there are some possibilities of drawing nice boxes around your sequence homologies using a spreadsheet or a word-processor. The main disadvantage however is that you have to do it by hand which is a very tedious work (i know that by experience). So i think any program facilitating this would be of great help for many of us. If there are programs out there, no matter what OS they are for, please make them available! 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. Output is suitable either for LJ250 color printer or as a UIS file for later conversion with DEC's RENDER-program supplied with VWS. The latter format can be converted into almost anything important on VAXes, including POSTSCRIPT. If anyone is interested in this, please write. My address is Kay Hofmann BUDI.gen1.genetik.uni-koeln.de
roy@phri.nyu.edu (Roy Smith) (04/03/91)
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!"