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.

Motif discovery
MEME	Find ungapped motifs in unaligned sequences	Sample output
Glam2	Find gapped motifs in unaligned sequences	Sample output, Manual, Tutorial
Motif search
AMA	Print the Average Affinity Score of each sequence in a database.	Sample output
Beadstring	Searches a sequence database for a given collection of motifs. The motifs are represented using a hidden Markov model with a linear topology, thus requiring that the motifs appear in a specified order.	Sample output
FIMO	Searches 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	Searches a sequence database for occurences of known motifs. This program assumes exactly one occurrence of a motif per sequence, and each sequence in the database is assigned a p-value, which is based on the product of the p-values of the individual motif occurrences in that sequence.	Sample output
MCAST	Searches a sequence database for clusters of known motifs. Like beadstring and miao, `mcast` employs a motif-based hidden Markov model, but uses a star topology and a novel scoring algorithm. The motifs may appear in any order.	Sample output
MIAO	Searches a sequence database for clusters of known motifs. As in `beadstring` motifs are represented using a hidden Markov model, but `miao` uses the complete or star topologies. This allows the motifs to appear in any order.	Sample output
Motif comparison
Tomtom	Search one or more motifs against a database of known motifs.	Sample output
Motif function analysis
GOMO	Identify possible roles (Gene Ontology terms) for DNA binding motifs.	Sample output
Motif database conversion utilities
chen2meme	Convert a CHEN matrix file to MEME output format.
iupac2meme	Convert an IUPAC string to MEME output format.
jaspar2meme	Convert a directory of JASPAR files to MEME output format.
scpd2meme	Convert an SCPD matrix file to MEME output format.
priority2meme	Convert a PRIORITY matrix file to MEME output format.
tamo2meme	Convert a TAMO matrix file to MEME output format.
transfac2meme	Convert a TRANSFAC matrix file to MEME output format.
uniprobe2meme	Convert a UNIPROBE matrix file to MEME output format.
Assorted utilities
alphtype	Classifies a string passed as a command line argument as an instance of the DNA or Protein alphabet.
ceqlogo	Create motif logos.
clustalw2fasta	Convert a Clustalw multiple alignment into FASTA format.
clustalw2phylip	Convert a Clustalw multiple alignment into Phylip format.
draw-mhmm	Convert a motif-based HMM into a format suitable for drawing by graphviz.
fasta-get-markov	Estimate a Markov model from a FASTA file of sequences.
fasta-io	Reads and writes FASTA files.
fitevd	Fits an Extreme Value Distribution to data.
gendb	Generates sequences from a Markov model.
getsize	Print statistics about sequences read from a FASTA file.
glam2format	Converting glam2 motifs to standard alignment formats.
psp-gen	Generate position-specific priors from positive (likely to contain a feature of interest) and negative sequences (unlikely to contain a feature of interest) 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.
log-hmm	Convert a motif-based HMM from probabilities to log probabilities.
meme-io	Prints summary of MEME HTML file to standard out as plain text.
mast2txt	Creates a plain text MAST output from the xml output.
mhmm	This program creates motif-based hidden Markov models (HMMs) of families of related biosequences. The program takes as input a set of DNA or protein motif models constructed by MEME and produces as output a single HMM containing the given motifs.
mhmme	Randomly generate sequences according to a given hidden Markov model.
mhmms	mhmms searches a sequence database using a Meta-MEME motif-based hidden Markov model (HMM) of the kind produced by mhmm.
obo2dag	Generate a GO DAG file from a Gene Ontology OBO file.
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.
readseq	Format conversion utility for sequence data.
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

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: