MEME Suite

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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

Homepage

http://meme-suite.org/index.html