
                               README

=============================================================================
                           Introduction             
=============================================================================
The  MEME suite 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 
suite represents motifs as position-dependent scoring matrices. 

The MEME suite consists of programs which allow you to: 
  meme      - for discovery of motifs shared by a group of sequences, 
  mast      - for search of databases for sequences containing these motifs,
  tomtom    - for searching databases of motifs for similar motifs,
  gomo      - for finding Gene Ontology terms linked to the motifs,
  glam2     - for discovery of gapped motifs,
  glam2scan - for scanning sequences with gapped motifs,
  fimo      - for scanning sequences with motifs,
  mcast     - for finding motif clusters,
  meme-chip - for analysis of large DNA datasets like ChIPseq output,
  spamo     - for finding motif complexes by analysing motif spacing,
  dreme     - for discovery of short regular expression motifs,
and that's just the web enabled tools.

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

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

To cite the full MEME suite, please cite:
    Timothy L. Bailey, Mikael Bodén, Fabian A. Buske, Martin Frith, 
    Charles E. Grant, Luca Clementi, Jingyuan Ren, Wilfred W. Li, 
    William S. Noble, "MEME SUITE: tools for motif discovery and searching", 
    Nucleic Acids Research, 37:W202-W208, 2009.

To cite individual tools, please check the citation page:
    http://meme.nbcr.net/meme/doc/cite.html

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

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                          Documentation 
=============================================================================
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
=============================================================================
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: 

    meme@nbcr.net

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

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

1. Clone from bitbucket (you have to be granted access to this mercurial repository):
    hg clone ssh://hg@bitbucket.org/tlbailey/meme

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 --enable-web --enable-opt --enable-build-libxml2 --enable-build-libxslt
    make dist

