What is MEME Suite?
MEME Suite is a collection of tools for the discovery of novel motifs in groups of unaligned nucleotide or protein sequences and, a wide variety of motif-based analyses. It supports motif-based analysis of DNA, RNA and protein sequences.
- Motif Discovery: MEME, MEME-ChIP, DRMEM, GLAM2
- Motif Enrichment Analysis: AME, CentriMo, SpaMo, GOMO
- Motif Search: FIMO, MAST, MCAST, MOTIPH, GLAM2Scan
- Motif Comparison: Tomtom
- Additional Primary Tools: AMA
- Motif Format Conversion Scripts: beeml2meme, chen2meme, elm2meme, iupac2meme, jaspar2meme, matrix2meme, meme2meme, nmica2meme, priority2meme, rna2meme, scpd2meme, sites2meme, taipale2meme, tamo2meme, transfac2meme, uniprobe2meme
- File Format Conversion Utilities: clustalw2fasta, clustalw2phylip, glam2format, obo2dag
- Other Utilities:alphtype, ama-qvalues, ceqlogo, compute-prior-dist, create-priors, dust, fasta-center, fasta-dinucleotide-shuffle, fasta-get-markov, fasta-grep, fasta-shuffle-letters, fasta-subsample, fitevd, gendb, getsize, glam2mask, etc.
Using MEME Suite
The MEME Suite is installed under /share1/meme/ in our cluster systems. The database directory is located at /share1/meme/db in which Motif databases and GOMO databases are provided. Please note that sequence databases are not installed in our system. User can download specific sequence database upon your requirements with links provided at http://meme-suite.org/db/sequences.
| System | Version | Command |
|---|---|---|
| HPC2015 | 4.11.2 | module load meme/impi/4.11.2 |
Additional Information
Official MEME Website: http://meme-suite.org/
MEME Suite Manual: http://meme-suite.org/doc/overview.html
Sequence Databases: http://meme-suite.org/db/sequences