May 8, 1994. A script helping create sequence logos from multiple sequence alignments. ------------------------------------------------------------------------- Programs alpro and makelogo create a sequence logo from a file of multiply aligned sequences. A sequence logo is a post-script file graphically showing the patterns in a multiple alignment together with their information content (see article "Sequence logos: a new way to display consensus sequences" by Schneider and Stephens in Nucleic Acids Res., 18(20):6097-6100, 1990). The programs were written by Tom Schneider and are available by anonymous ftp at "ftp.ncifcrf.gov" (in /pub/delila) and at "bioinformatics.weizmann.ac.il" (in /pub/software/seqlogos. These programs use a number of parameter files and their input and output files have fixed names. I wrote a shell script "logoaid" to help produce sequence logos with the programs. The shell is not too complicated but lengthy (1009 lines), partly because I tried to keep it well annotated and partly because I tried to keep it simple. The shell can certainly be improved but as far as I used and checked it it works fine. In addition to the makelogo and alpro programs the script optionally uses the readseq program (a program to reformat sequences [d.g.gilbert gilbertd@bio.indiana.edu]), a text editor, a text viewer and a post-script file viewer. The shell offers to show help files on a few topics and demo files for some of the required files. These files are available together with the shell script by anonymous ftp at "bioinformatics.weizmann.ac.il" (in /pub/software/logoaid) and at "ftp.ncifcrf.gov" (in /pub/delila/logoaid). Please send me any suggestions and comments you have about the script. Shmuel -- Shmuel Pietrokovski ! Structural Biology department ! bppietro@dapsas1.weizmann.ac.il Weizmann Institute of Science ! fax: ##972 (8) 344105 76100 Rehovot - ISRAEL ! tel: ##972 (8) 343367