文件列表:

meme_3.5.4\aclocal.m4 (30855, 2006-09-22)
meme_3.5.4\AUTHORS (38, 2006-09-22)
meme_3.5.4\bootstrap (1751, 2006-09-22)
meme_3.5.4\ChangeLog (8568, 2006-09-22)
meme_3.5.4\config\config.guess (39715, 2006-09-22)
meme_3.5.4\config\config.sub (29483, 2006-09-22)
meme_3.5.4\config\depcomp (12123, 2006-09-22)
meme_3.5.4\config\install-sh (5569, 2006-09-22)
meme_3.5.4\config\missing (10270, 2006-09-22)
meme_3.5.4\config\mkinstalldirs (1801, 2006-09-22)
meme_3.5.4\config.h (5618, 2008-09-18)
meme_3.5.4\config.h.in (5269, 2006-09-22)
meme_3.5.4\config.log (34140, 2009-03-17)
meme_3.5.4\config.status (41354, 2009-03-17)
meme_3.5.4\configure (224558, 2006-09-22)
meme_3.5.4\configure.ac (15005, 2006-09-22)
meme_3.5.4\COPYING (1904, 2006-09-22)
meme_3.5.4\etc\Makefile (9642, 2009-03-17)
meme_3.5.4\etc\Makefile.am (2702, 2006-09-22)
meme_3.5.4\etc\Makefile.in (9512, 2006-09-22)
meme_3.5.4\etc\mast.doc (17219, 2006-09-22)
meme_3.5.4\etc\mast_db.list (9864, 2006-09-22)
meme_3.5.4\etc\mast_upstream_db.list (1286, 2006-09-22)
meme_3.5.4\etc\meme-explanation.html (17900, 2006-09-22)
meme_3.5.4\etc\meme.csh (738, 2008-09-18)
meme_3.5.4\etc\meme.csh.in (746, 2006-09-22)
meme_3.5.4\etc\meme.darwin.in (855, 2006-09-22)
meme_3.5.4\etc\meme.doc (24426, 2006-09-22)
meme_3.5.4\etc\meme.irix.in (1732, 2006-09-22)
meme_3.5.4\etc\meme.linux (1970, 2008-09-18)
meme_3.5.4\etc\meme.linux.in (1974, 2006-09-22)
meme_3.5.4\etc\meme.sh (1005, 2008-09-18)
meme_3.5.4\etc\meme.sh.in (1013, 2006-09-22)
meme_3.5.4\etc\meme.solaris.in (2027, 2006-09-22)
meme_3.5.4\etc\prior1.plib (314, 2006-09-22)
meme_3.5.4\etc\prior30.plib (9706, 2006-09-22)
meme_3.5.4\etc\StartupParameters.plist (72, 2006-09-22)
meme_3.5.4\INSTALL (566, 2006-09-22)
meme_3.5.4\m4\functions.m4 (1818, 2006-09-22)
meme_3.5.4\m4\headers.m4 (1919, 2006-09-22)
... ...

README ============================================================================= Introduction ============================================================================= 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), 19***. ============================================================================= Installation ============================================================================= See INSTALL for operating system requirements, prerequisite software, and installation instructions. ============================================================================= 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 /web/ directory. ============================================================================= 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. ============================================================================= Problems and comments ============================================================================= Please address any problems or comments to: tbailey@imb.uq.edu.au or meme@nbcr.net ============================================================================= Release Notes ============================================================================= See file /web/release_notes.html ============================================================================= Developers Notes ============================================================================= 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://meme@summit.ucsd.edu/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

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