A script helping create sequence logos from multiple sequence alignments

Shmuel Pietrokovski bppietro at dapsas1.weizmann.ac.il
Mon May 9 02:49:18 EST 1994

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),
because I tried to keep it well annotated and partly because I tried to
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
the readseq program (a program to reformat sequences Ýd.g.gilbert
gilbertd at bio.indiana.edu¨), a text editor, a text viewer and a
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 Pietrokovski                 !
 Structural Biology department       ! bppietro at dapsas1.weizmann.ac.il
 Weizmann Institute of Science       ! fax: ##972 (8) 344105
 76100 Rehovot - ISRAEL              ! tel: ##972 (8) 343367

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