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 | |||
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 | |
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 | |
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 | |
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 | |
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 | |
Glam2Scan | Search for occurences of gapped motifs, discovered by GLAM2. | Sample output, Manual | |
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 | |
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. | ||
glam2mask | Mask glam2 motifs out of sequences, so that weaker motifs can be found. | ||
jaspar2meme | Convert a directory of JASPAR files to MEME output format. | ||
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. | ||
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. | ||
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. | ||
select-star-species | Tries to find the subset of species whose subtree is "closet" to a start topology. | ||
shadow | Perform phylogenetic shadowing on a given DNA alignment, using a given tree. | ||
transfac2meme | Convert a TRANSFAC matrix file to MEME output format. |
File formats
- FASTA sequence files (with a sample),
- clustalw alignment files
- motif file (with a sample),
- background file,
- TRANSFAC file.
- GLAM2 alphabet files,
- GLAM2 Dirichlet mixture files,
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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