MEME Suite
Description
The MEME Suite allows the biologist to discover novel motifs in collections of unaligned nucleotide or protein sequences, and to perform a wide variety of other motif-based analyses. The MEME Suite supports motif-based analysis of DNA, RNA and protein sequences. It provides motif discovery algorithms using both probabilistic (MEME) and discrete models (MEME), which have complementary strengths. It also allows discovery of motifs with arbitrary insertions and deletions (GLAM2). In addition to motif discovery, the MEME Suite provides tools for scanning sequences for matches to motifs (FIMO, MAST and GLAM2Scan), scanning for clusters of motifs (MCAST), comparing motifs to known motifs (Tomtom), finding preferred spacings between motifs (SpaMo), predicting the biological roles of motifs (GOMo), measuring the positional enrichment of sequences for known motifs (CentriMo), and analyzing ChIP-seq and other large datasets (MEME-ChIP).
License
http://meme-suite.org/doc/copyright.html?man_type=web
Usage
Upcoming modulesystem change alert!
Due to large number of applications and their versions it is not practical to keep them explicitly listed at our wiki pages. Therefore an upgrade of modulefiles is underway. A feature of this upgrade will be the existence of default module for every application. This default choice does not need version number and it will load some (usually latest) version.
You can test the new version now by adding a line
source /cvmfs/software.metacentrum.cz/modulefiles/5.1.0/loadmodules
to your script before loading a module. Then, you can list all versions of meme-suite and load default version of meme-suite as
module avail meme-suite/ # list available modules module load meme-suite # load (default) module
If you wish to keep up to the current system, it is still possible. Simply list all modules by
module avail meme-suite
and choose explicit version you want to use.
Available binaries are:
ame centrimo dreme dreme-py3 dust fimo glam2 glam2scan gomo mast mcast meme meme-chip momo purge spamo tomtom
Notice: Sequence databases (gomo_batabases and motif_databases) are localized in the path:
/software/meme-suite/5.0.1-mpi/db
Instead of meme ... -p 2 you can use command mpirun meme without -p parametr. Number of cpus will be taken from PBS system in this case.
Documentation
Documentation is available at http://meme-suite.org/doc/overview.html?man_type=web