Multiple EM for Motif Elicitation (MEME) Version 3.0

Technology Description of MEME Version 3.0
MEME allows the user to discover motifs in groups of related DNA or protein sequences, and MAST enables the user to further search databases for sequences containing these motifs. They are copyrighted software and can be licensed for commercial use separately or together for reasonable fees. Executable software (http://meme.nbcr.net/downloads/) can be downloaded.

MEME 3.0 – Multiple Eexpectation-maximization for Motif Elicitation, see MEME Site License.

MEME Method

The input to MEME is a set of unaligned DNA or protein sequences (the training set) and outputs as many motifs as requested. MEME uses statistical modeling techniques to automatically choose the best width and description of each motif.

For each motif it discovers, MEME reports the occurrences (sites), consensus sequence and the level of conservation (information content) at each position in the pattern. A typical MEME motif is shown below.

MEME also produces block diagrams showing where all of the discovered motifs occur in the training set sequences. This illuminates the spatial arrangement of protein domains or DNA features (e.g. protein binding sites) within the input sequences. A typical MEME block diagram is shown below.

MEME Operations

  • MEME finds motifs by identifying highly correlated stretches of letters in the input sequences.
  • MEME then applies statistical models to validate the most significant motifs contained within the input sequences.
  • Lastly, MEME reports an E-value for each motif, giving a measure of the motif's validity (likelihood of not being a random sequence artifact).

MEME Utilities

MEME motifs can predict/explain function, homology and structure of sequences. MEME can aid in discovery of protein binding sites and other regulatory elements in groups of upstream regions from co-regulated genes.

MAST 3.0 – Motif Alignment and Search Tool: MAST Site License

MAST Operations

  • MAST searches biological sequence libraries for sequences that match the motifs discovered by MEME (or similar tool).
  • MAST outputs the names of library sequences in order of the number of matches to the motifs in the group.
  • MAST outputs motif diagrams showing motif order and spacing within each matching library sequence.
  • MAST outputs detailed annotation of each matching sequence, showing the location and strengths of motif sequence matches.

System Requirements

MEME and MAST operate on many platforms, including Linux, Mac OSX, Cygwin (running under Windows) and some types of UNIX. A list of supported operating systems and their manufactures is available at http://meme.sdsc.edu/meme/meme-install.html#sysrequirements


System Information

A detailed overview of MEME and MAST is located at System Release Notes.

Commercial use site licenses may be downloaded at the following links:
MEME 3.0 – Multiple Expectation-maximization for Motif Elicitation: MEME Site License
MAST 3.0 – Motif Alignment and Search Tool: MAST Site License

Executable software can be downloaded for licensed use at the following link:
http://meme.nbcr.net/downloads/

Case Numbers: SD2001-804 (MEME 3.0), SD2002-802 (MAST 3.0)


Keywords: MEME, MAST, Motif


Inquiries To:  invent@ucsd.edu