CorreLogo is a program for generating 3D sequence logos for a given RNA or DNA sequence alignment.

INSTALLATION:

1. unzip the obtained tar file:
   unzip correlogo.tar.gz
2. extract the tar archive:
   tar xvf correlogo.tar
3. Define the obtained directory in the environment variable $CORRELOGO_HOME:
   setenv CORRELOGO_HOME completepathname   # using C-shell
   export CORRELOGO_HOME=completepathname   # using bash 
4. change the current working directory:
   cd $CORRELOGO_HOME/src
5. Compile the sources with the command:
   make
6. Copy the binary called correlogo into $CORRELOGO_HOME/bin
7. Optionally add the directory $CORRELOGO_HOME/bin to your PATH variable:
   setenv PATH $PATH":$CORRELOGO_HOME"    # using C-shell : add this line you your .cshrc file in your home directory
   export PATH=$PATH":$CORRELOGO_HOME"    # using bash : add this line to your .bashrc file in your home directory. On a Mac (OS X) this file will instead be called .bash_profile
   Alternatively you can copy the correlogo binary to a location that is already parth of your PATH variable.
	Finished!

Usage:

Start correlogo with the unix command line:
correlogo -i <YOUR_FASTA_FILE>

This implies that the environment variable $CORRELOGO_HOME is correctly set and that the binary to the correlogo program could be found. Otherwise the complete path to the correlogo binary has to be specified and the option -b should be set to -b YOUR_CORRELOGO_DIR/resources/correlogo_bitmaps.dat . The program should then generate several different output files.

CorreLogo generates by default four output files a given sequence alignment: 1. JVX file format (ending .jwx, readable by the JavaView application available under www.javaview.de); 2. VRML 2.0 output (ending .wrl, readable by VRML 2.0 or VRML 97 viewers); 3. A file containing mutual information values as ASCII text representing a square matrix (ending .matrix); 4 A text file that corresponds to the text output of the Correlogo web server.
The sequence alignment has to be in FASTA format.

Running correlogo without command line options (command: correlogo) shows a help message similar to this readme file.

An example regarding a sequence alignment of tRNA can be run like this:
cd YOUR_CORRELOGO_INSTALLATION_DIR/example
./run_example.sh

Please refer to our publication for more details regarding the method:

Bindewald, E., Schneider, T.D. and Shapiro, B.A.
CorreLogo: An online server for 3D sequence logos or RNA and DNA alignments.
Nucleic Acids Research. 2006, 34(Web Server issue):W405-11.

For questions and comments send emails to:

Eckart Bindewald
eckart@mail.nih.gov
