The MEME suite of motif-based sequence analysis tools

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 sequences	Sample output
DREME	Find short motifs in large sets of sequences
Glam2	Find gapped motifs in unaligned sequences	Sample output, Manual, Tutorial
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
Glam2Scan	Search for occurences of gapped motifs, discovered by GLAM2.	Sample output, Manual
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
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.
AME	Perform a motif enrichment analysis, outputting the names of known DNA motifs that are enriched in the input sequences.
CentriMo	Identify centrally enriched motifs.
CentriMo Plots	Generate plots for CentriMo output.
GOMO	Identify possible roles (Gene Ontology terms) for DNA binding motifs.
MEME ChIP	Automate analysis of ChIP-seq data using the MEME suite.
Tomtom	Search one or more motifs against a database of known motifs.	Sample output
SpaMo	Find enriched motif spacings.
File format conversion utilities
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.
Assorted 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.
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.
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.
pmb_bf	Calculate the statistical power of phylogentic motif models.
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: