The MEME (Multiple Em for Motif Elicitation) Suite allows the biologist to discover novel motifs in collections of unaligned nucleotides or protein sequences, and to perform a wide variety of other motif-based analyses. Such motifs encode many biological functions, and their detection and characterization is important in the study of molecular interactions in the cell, including the regulation of gene expression.
MEME discovers novel, ungapped motifs (recurring, fixed-length patterns) in our sequences (sample output from sequences). MEME splits variable-length patterns into two or more separate motifs.
MEME takes a group of DNA or protein sequences as input and outputs as many motifs as requested up to a user-specified statistical confidence threshold. MEME uses statistical modeling techniques to automatically choose the best width, number of occurrences, and description for each motif.
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 favoured 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 freely available for academic use.
The MEME Suite is a collection of tools that work together. Motif Discovery tools are;
- Motif Enrichment Analysis
- Motif Search
- Motif Comparison
- Gene Regulation
- Additional Primary Tools
- Motif Format Conversion Scripts
- File Format Conversion Utilities
- FASTA Sequence Utilities
The MEME algorithm has been widely used for the discovery of DNA and protein sequence motifs, and MEME continues to be the starting point for most analyses using the MEME Suite.
Once we have discovered a collection of motifs, we may wish to perform additional analyses to better characterize those motifs. The MEME Suite provides three types of tools for carrying out such analyses. First, the MEME Suite can compare our DNA motifs to known compendia of motifs (such as JASPAR, Flyreg and DPINTERACT) to see if our motif is similar to a known regulatory motif. This type of analysis is done using Tomtom. Second, the MEME Suite can attempt to determine what types of regulatory functions our motif might be involved in. Third, the MEME Suite can search a sequence database for additional occurrences of your motif.
The MEME output for each reported motif has a button for submitting that motif directly to Tomtom. The Tomtom web application also allows the user to submit a motif by pasting in columns of base counts for each position of the motif. The user then selects the motif similarity measure to use and chooses which online motif database to search.
The output of Tom-tom includes LOGOS representing the alignment of two motifs, the p-value and q-value of the match, and links back to the parent motif database for more detailed information about the target motif.