MEME - Introduction

MEME -- Multiple EM for Motif Elicitation

Motif discovery tool


MEME is a tool for discovering motifs in a group of related DNA or protein sequences.

A motif is a sequence pattern that occurs repeatedly in a group of related protein or DNA sequences. MEME represents motifs as position-dependent letter-probability matrices which describe the probability of each possible letter at each position in the pattern. Individual MEME motifs do not contain gaps. Patterns with variable-length gaps are split by MEME into two or more separate motifs.

MEME takes as input a group of 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 for each motif. For each motif MEME discovers, there are seven outputs:

  1. A summary line showing the width and estimated number of occurrences of the motif in the training set.
  2. A simplified letter-probability matrix.
  3. A diagram showing the degree of conservation at each motif position.
  4. A multilevel consensus sequence showing the most conserved letter(s) at each motif position.
  5. A position-dependent scoring matrix for use by the MAST database search program.
  6. The motif letter-probability matrix.

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