The MEME Suite allows the biologist to discover novel motifs in collections of unaligned DNA or protein sequences and to search for motif occurrences in sequence databases. The suite is comprised of a collection of tools that work together, as shown below. Not all the tools are avaliable as webservices, so to get the full power of the MEME Suite you will need to download and install a local copy of the software.

Motif Discovery
MEME Find ungapped motifs in unaligned DNA, RNA or protein sequences. Sample output
MEME ChIP Automate analysis of ChIP-seq and other large DNA datasets using the MEME suite. Sample output,
DREME Find short motifs in large sets of DNA or RNA sequences. Also allows discriminative motif analysis using a set of control sequences. Sample output
Glam2 Find gapped motifs in unaligned DNA or protein sequences. Sample output, Manual, Tutorial
Motif Enrichment Analysis
AME Motif Enrichment Analysis: find known DNA motifs that are enriched in the input sequences.  
CentriMo Central Motif Enrichment Analysis: Find motifs that are enriched near the centers of equal-length sequences. Sample output,
SpaMo Motif Spacing Analysis: Find known motifs that occur with preferred spacings relative to a primary motif in a set of DNA sequences. Sample output,
GOMO Genome Ontology Motif Enrichment: Identify possible roles (Gene Ontology terms) for DNA binding motifs.  
Motif Search
FIMO Search a sequence database for occurrences of known motifs. This program treats each motif independently and reports all putative motif occurrences below a specified p-value threshold. Sample output
MAST Search a sequence database for occurences of known motifs. This program assumes exactly one occurrence of each motif per sequence, and each sequence in the database is assigned a p-value, based on the product of the p-values of the individual motif occurrences in that sequence. Sample output
MCAST Search a sequence database for clusters of known motifs. mcast employs a motif-based hidden Markov model, using a star topology and a novel scoring algorithm. The motifs may appear in any order. Sample output
Glam2Scan Search for occurences of gapped motifs, discovered by GLAM2. Sample output, Manual
Motif Comparison
Tomtom Find motifs that are similar to a given DNA motif by searching a database of known motifs. Sample output
Additional Primary Tools
AMA Print the Average Motif Affinity score of each sequence in a database. The score is calculated by averaging the likelihood ratio scores for all feasible binding events to the given sequence and to its reverse strand.  
File Format Conversion Utilities
beeml2meme Convert an BEEML matrix file to MEME format.
chen2meme Convert a CHEN matrix file to MEME format.
clustalw2fasta Convert a Clustalw multiple alignment into FASTA format.
clustalw2phylip Convert a Clustalw multiple alignment into Phylip format.
glam2format Convert glam2 motifs to standard alignment formats.
obo2dag Convert a Gene Ontology OBO file into a GO DAG file.
iupac2meme Convert an IUPAC string to MEME format.
jaspar2meme Convert a directory of JASPAR files to MEME format.
mast2txt Convert MAST XML output into plain text.
meme2meme Convert and merge multiple MEME formatted files.
priority2meme Convert a PRIORITY matrix file to MEME format.
readseq Format conversion utility for sequence data.
rna2meme Convert a FASTA file with short RNA sequences into motifs for DNA they might bind in MEME format.
scpd2meme Convert an SCPD matrix file to MEME format.
tamo2meme Convert a TAMO matrix file to MEME format.
transfac2meme Convert a TRANSFAC matrix file to MEME format.
uniprobe2meme Convert a UNIPROBE matrix file to MEME format.
Other Utilities
alphtype Classify a string passed as a command line argument as an instance of the DNA or protein alphabet.
ama-qvalues Add q-values to ama output.
ceqlogo Create motif logos.
compute-prior-dist Compute the distribution of priors in a MEME PSP format file. Sample output
fasta-get-markov Estimate a Markov model from a FASTA file of sequences.
fasta-io Read and write FASTA files.
fasta-subsample Extract a random selection of the sequences in a FASTA file. Can also subsample the sequences themselves.
fitevd Fit an extreme value distribution to data.
gendb Generate sequences from a Markov model.
getsize Print statistics about sequences read from a FASTA file.
glam2mask Mask glam2 motifs out of sequences, so that weaker motifs can be found.
gomo_highlight Identify GO terms which are implied by other GO terms, allowing the most specific GO terms to be highlighted in the conversion to html.
meme-io Print summary of MEME HTML file to standard output as plain text.
meme-rename Easily rename MEME Suite HTML files to unique names incorporating the path name (rather than "meme.html").
pmb_bf Calculate the statistical power of phylogentic motif models.
psp-gen Generate position-specific priors from positive (likely to contain a feature of interest) and negative (unlikely to contain a feature of interest) sequences for use as an additional input to MEME.
purge Remove highly similar members of a set of sequences.
qvalue Compute q-values from p-values.
reconcile-tree-alignment Given a tree and an alignment, identify the intersection of the sets of sequence IDs and leaf labels. Trim the extra sequences and leaves and print the resulting alignment and tree.
reduce-alignment Extract specified columns from a multiple alignment.
remove-alignment-gaps Remove from an alignment all columns that correspond to a gap in a specified species.
shadow Perform phylogenetic shadowing on a given DNA alignment, using a given tree.

File formats

Accessing MEME Suite web applications from scripts

Installation instructions.

Release notes.

Visit the MEME Suite home page.

Maintenance and development of the MEME Suite is funded by the National Center for Research Resources grant NIH/NCRR R01 RR021692. The MEME Suite web server is funded by the National Biomedical Computation Resource.

Developed and maintained by:
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