readme

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                               README

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                           Introduction             
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The  MEME system provides online tools for discovering  and using protein and 
DNA sequence motifs.  A motif is a pattern of nucleotides or amino acids that 
appears repeatedly in a group of related  DNA or protein sequences.  The MEME 
system represents motifs as position-dependent scoring matrices. 

The MEME system consists of two programs which allow you to: 
  meme - for discovery of motifs shared by a group of sequences and, 
  mast - for search of databases for sequences containing these motifs. 

You can download the ANSI C source code for MEME system from
http://meme.nbcr.net/meme/meme-download.html

You can also use the MEME system via its website at http://meme.nbcr.net

If you use MEME in your research, please cite: 
    Timothy  L. Bailey  and Charles Elkan,  "Fitting a mixture model
    by expectation  maximization to discover  motifs in biopolymers",
    Proceedings of the Second International Conference on Intelligent
    Systems for Molecular Biology, (28-36), AAAI Press, 1994. 

If you use MAST in your research, please cite: 
    Timothy L. Bailey and Michael Gribskov, "Combining evidence using 
    p-values: application to sequence homology searches", Bioinformatics, 
    14(48-54), 1998.

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                          Installation         
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See INSTALL for operating system requirements, prerequisite software, 
and installation instructions.

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                          Documentation 
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Documentation is available online at http://meme.nbcr.net/meme
If you did installation with the --enable-web switch, the html documentation
will be installed in your <install-path>/web/ directory. 

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                        Using MEME/MAST
=============================================================================
Before using MEME and mast, users must add a few environment variables.
All needed variables are defined in meme.csh and meme.sh files.

(1) if using csh and tcsh, execute the following command:
    source $prefix/etc/meme.csh   

    To make the addition of these variabls automatic add a line to 
	your .cshrc or .tcshrc file:
    source $prefix/etc/meme.csh     

(2) if using sh or bash, execute the following command:
    . $prefix/etc/meme.sh 

    To make the addition of these variabls automatic add a line to 
	your .profile or .bash_profile file:
    . $prefix/etc/meme.sh   

The $prefix in the commands above is a full path to the installation directory.

To find out how to use MEME or MAST execute:
    meme
or
    mast

The usage will be printed on stdout.

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                      Problems and comments 
=============================================================================
Please address any problems or comments to: 
    [e-mail]
or 
    [e-mail]

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                          Release Notes 
=============================================================================
See file <install-path>/web/release_notes.html

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                          Developers Notes
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Detailed notes are given in the MEME wiki: 
  https://nbcr.net/pub/wiki/index.php?title=MEME_Developers%27_Guide

1. Check out from svn (you have to have read/write access to this svn):
    svn checkout svn+ssh://[e-mail]/meme/SVNROOT/trunk

2. To create a distribution tar ball meme_VERSION.tar.gz.  (Note: the
	version number is set in configure.ac using variable
	AM_INIT_AUTOMAKE.)
    cd trunk
    ./bootstrap
    ./configure
    make dist

3. Whenever databases are added to MAST:
	1) add the database to website/mast.html
	2) add the database to website/mast-databases.html
	3) add the database to etc/mast_db.list or etc/mast_upstream_db.list