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. 2006 Jul 1;34(Web Server issue):W369-73.
doi: 10.1093/nar/gkl198.

MEME: Discovering and Analyzing DNA and Protein Sequence Motifs

Free PMC article

MEME: Discovering and Analyzing DNA and Protein Sequence Motifs

Timothy L Bailey et al. Nucleic Acids Res. .
Free PMC article


MEME (Multiple EM for Motif Elicitation) is one of the most widely used tools for searching for novel 'signals' in sets of biological sequences. Applications include the discovery of new transcription factor binding sites and protein domains. MEME works by searching for repeated, ungapped sequence patterns that occur in the DNA or protein sequences provided by the user. Users can perform MEME searches via the web server hosted by the National Biomedical Computation Resource ( and several mirror sites. Through the same web server, users can also access the Motif Alignment and Search Tool to search sequence databases for matches to motifs encoded in several popular formats. By clicking on buttons in the MEME output, users can compare the motifs discovered in their input sequences with databases of known motifs, search sequence databases for matches to the motifs and display the motifs in various formats. This article describes the freely accessible web server and its architecture, and discusses ways to use MEME effectively to find new sequence patterns in biological sequences and analyze their significance.


Figure 1
Figure 1
Sample MEME output.This portion of an MEME HTML output form shows a protein motif that MEME has discovered in the input sequences. The sites identified as belonging to the motif are indicated, and above them is the ‘consensus’ of the motif and a color-coded bar graph showing the conservation of each position in the motif. Some of the hyperlinked buttons that allow the motif to be viewed and analyzed in other ways can be seen at the bottom of the screen shot.
Figure 2
Figure 2
LOGO of protein motif. LOGOS are a visualization tool for motifs. The height of a letter indicates its relative frequency at the given position (x-axis) in the motif.
Figure 3
Figure 3
Usage of MEME at the NBCR web server. The plot shows the number of different users submitting jobs to the NBCR MEME web server each month since December 2000. Usage figures for March 2006 include up to March 20 only.

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