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).

Availability

Version 5.0.1 is freely available for MetaCentrum users

meme-suite-5.0.1-mpi

Licence

http://meme-suite.org/doc/copyright.html?man_type=web

Use

Environment initialization:

module add meme-suite-5.0.1-mpi

Warning.gif WARNING: Use MEME-suite only on Debian9 machines!

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

Program manager

meta@cesnet.cz

Homepage

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