May 8, 1994.
A script helping create sequence logos from multiple sequence alignments.
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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 Ýd.g.gilbert
gilbertd at 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 at dapsas1.weizmann.ac.il
Weizmann Institute of Science ! fax: ##972 (8) 344105
76100 Rehovot - ISRAEL ! tel: ##972 (8) 343367
