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EDIT: This is a hacked version of the MEME bioinformatics suite, which has been modified to include an extra "--allow-overlap" flag to "FIMO". This extra flag is required for SNP CRM annotation to work (see https://github.com/tomwhi/snpCrmAnnotation). If you are looking for the official MEME suite software, this is not what you are looking for - please go to http://meme-suite.org instead. ***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-suite.org/doc/download.html You can also use the MEME suite via its website at http://meme-suite.org . ***Citing*** 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-suite.org/doc/cite.html ***Installation*** See `doc/install.html` for operating system requirements, prerequisite software, and installation instructions. ***Documentation*** Documentation is available online at http://meme-suite.org/doc/overview.html otherwise look in the `doc/` folder for `overview.html` as a place to start. If you did installation with the `--enable-web` switch, the html documentation will be installed with the website at `<website>/meme_<version>/doc/overview.html`. ***Problems and comments*** Please address any problems or comments to: [email protected] or https://groups.google.com/forum/#!forum/meme-suite ***Release Notes*** See file `<distribution-path>/doc/release-notes.html` or after a basic install see `<install-path>/doc/release_notes.html` or for a website install see `<website>/meme_<version>/doc/release-notes.html` ***Developers Notes*** To prepare a new release. 1. Clone from bitbucket (you have to be granted access to this mercurial repository): > hg clone ssh://[email protected]/tlbailey/meme 2. Create a release branch (Note: the version number is set in configure.ac using variable AM_INIT_AUTOMAKE.): > hg branch meme_VERSION hg ci -m "Create release branch for VERSION" 3. Once you are ready to create a release candidate tag the current revision (this is used to determine the release date and release revision): > hg tag meme_VERSION_0 3.1. If you later have to create another release candidate after applying some patches then move the tag so that the release date and release revision are correct: > hg tag -f meme_VERSION_0 4. Create the example output files by building a copy of the MEME Suite, ensuring it is first in your path, and running create_examples.pl: > cd meme/doc/examples ./create_examples.pl scp examples.tgz http://meme-suite.org/meme-software/example-output/examples.tgz # ok so this line doesn't really work but you should get the intent 5. To create a distribution tar ball meme_VERSION.tar.gz. > cd meme hg purge --all ./bootstrap ./configure --enable-web --enable-opt --enable-build-libxml2 --enable-build-libxslt make dist
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