The MEME Suite allows the biologist to discover novel motifs in collections of unaligned nucleotide or protein sequences, and to perform a wide variety of other motif-based analyses.
The MEME Suite supports motif-based analysis of DNA, RNA and protein sequences. It provides motif discovery algorithms using both probabilistic (MEME) and discrete models (MEME), which have complementary strengths. It also allows discovery of motifs with arbitrary insertions and deletions (GLAM2). In addition to motif discovery, the MEME Suite provides tools for scanning sequences for matches to motifs (FIMO, MAST and GLAM2Scan), scanning for clusters of motifs (MCAST), comparing motifs to known motifs (Tomtom), finding preferred spacings between motifs (SpaMo), predicting the biological roles of motifs (GOMo), measuring the positional enrichment of sequences for known motifs (CentriMo), and analyzing ChIP-seq and other large datasets (MEME-ChIP).
The MEME Suite is comprised of a collection of tools that work together, as shown below. Not all the tools are available 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. To see what has changed recently you can peruse the release notes.
| Motif Discovery | ||
|---|---|---|
| MEME | Find ungapped motifs in unaligned DNA, RNA or protein sequences. | Sample |
| MEME-ChIP | Comprehensive motif analysis of large nucleotide datasets such as those from ChIP-seq or CLIP-seq experiments. | Sample |
| DREME | Find short, ungapped motifs in large sets of DNA or RNA sequences. Also allows discriminative motif analysis using a set of control sequences. | Sample |
| GLAM2 | Find gapped motifs in DNA or protein sequences. It has a tutorial. | Sample |
| Motif Enrichment Analysis | ||
| AME | Motif Enrichment Analysis: find known DNA or RNA motifs that are relatively enriched in the input sequences compared to shuffled version of those sequences or control sequences. | Sample |
| CentriMo | Local Motif Enrichment Analysis: Find motifs that are enriched in local regions in equal-length sequences. | Sample |
| SpaMo | Motif Spacing Analysis: Find known motifs that occur with preferred spacings relative to a primary motif in a set of DNA sequences. | Sample |
| GOMO | Genome Ontology Motif Enrichment: Identify possible roles (Gene Ontology terms) for DNA binding motifs. | Sample |
| 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 |
| 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 |
| 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 |
| MOTIPH | Search a set of aligned sequences for conservered matches to motifs. In addition to the aligned sequences and the motifs, this program requires a maximum likelihood phylogenetic tree estimating the evolutionary relationships and distances among the sequences. | Sample |
| GLAM2Scan | Search for occurences of gapped motifs, discovered by GLAM2. | Sample |
| Motif Comparison | ||
| Tomtom | Find motifs that are similar to a given DNA or RNA motif by searching a database of known motifs. | Sample |
| 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. | |
| Motif Format Conversion Scripts | Foreign Motif Formats | |
| beeml2meme | Convert an BEEML matrix file to MEME format. | |
| chen2meme | Convert a CHEN matrix file to MEME format. | |
| elm2meme | Convert a ELM tab separated file to MEME format. | |
| iupac2meme | Convert an IUPAC string to MEME format. | |
| jaspar2meme | Convert a directory of JASPAR files to MEME format. | |
| matrix2meme | Convert count or frequency matrices to MEME format. | |
| meme2meme | Convert and merge multiple MEME formatted files. | |
| nmica2meme | Convert a nestedMICA (BioTiffin/XMS) matrix file to MEME format. | |
| priority2meme | Convert a PRIORITY matrix file to MEME format. | |
| 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. | |
| sites2meme | Convert files containing sites into MEME format. | |
| taipale2meme | Convert a tab-separated file exported from a spreadsheet of Taipale results 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. | |
| File Format Conversion Utilities | ||
| 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. | |
| 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 |
| create-priors | Compute priors and their distribution from raw scores in a Wiggle format file. | |
| dust | Mask low-complexity regions in DNA sequences in a FASTA file to N characters. | |
| fasta-center | Output the central portion of each sequence in a FASTA file of sequences. | |
| fasta-dinucleotide-shuffle | Shuffle the letters in each sequence in a file of FASTA file of nucleotide sequences, preserving the dinucleotide frequencies. | |
| fasta-get-markov | Estimate a Markov model from a FASTA file of sequences. | |
| fasta-hamming-enrich | Compute the relative enrichment of a regular expression in two sets of sequence, where the shortest Hamming distance is used to classify sequences. | |
| fasta-grep | Find matches to a Perl regular expression in a FASTA file of sequences. | |
| fasta-io | Read and write FASTA files. | |
| fasta-shuffle-letters | Shuffle the letters in each sequence in a file of FASTA file preserving k-mer frequencies. This makes use of uShuffle. | |
| 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 or (higher-order) shuffle 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. | |
| meme2alph | Extract the sequence alphabet definition from a MEME or DREME file (any format). | |
| meme-get-motif | Extract specified motifs from a MEME text (.txt) format file. | |
| 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. | |
| update-sequence-db | Create or update the sequence databases for a MEME Suite web server. | |
| File Formats | ||
| MEME Motif | The motif format which is supported by the MEME Suite. | |
| Alphabet Definition | A method for defining custom alphabets. | |
| Background Model | Background frequencies for DNA or protein sequences. | |
| Position-Specific Priors (PSP) | Priors (weights) on each position in each input sequence that can bias the search for motifs by MEME. | |
| Dirichlet Mixtures | A Dirichlet mixture file specifies residues' tendencies to align with one another, and is the basis for scoring columns of aligned residues in MEME and GLAM2. | |
| FASTA Sequence | DNA or protein sequences. | |
| ClustalW Alignment | A multiple alignment of DNA or protein sequences. | |
| Foreign Motif Formats | Motif formats that can be converted into MEME motifs using the motif format conversion scripts available when you install the MEME Suite on your own computer. | |
| GLAM2 Alphabet | A custom sequence alphabet for GLAM2. This can be used to provide alternate alphabets other than the standard DNA and protein. | |
| GO DAG | A file format which stores the structure of the Gene Ontology so it can be used to improve GOMO output. | |
| GOMO Output | The file format output by the GOMO tool. | |
| Guides and Tutorials | ||
| Web Service Access | How to access MEME Suite web services from Perl or Python scripts. | |
| Installation | How to install a local copy of the MEME Suite. | |
| Release notes | A list of changes included in the latest release. | |
Maintenance and development of the MEME Suite is funded by grant R01 GM103544 from the National Institutes of Health.
The MEME Suite web portal also receives support from Google.
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