UNIT 2.4 Discovering Novel Sequence Motifs with MEME

  1. Timothy L. Bailey

Published Online: 1 NOV 2002

DOI: 10.1002/0471250953.bi0204s00

Current Protocols in Bioinformatics

Current Protocols in Bioinformatics

How to Cite

Bailey, T. L. 2002. Discovering Novel Sequence Motifs with MEME. Current Protocols in Bioinformatics. 00:2.4:2.4.1–2.4.35.

Author Information

  1. University of Queensland, Brisbane, Australia

Publication History

  1. Published Online: 1 NOV 2002
  2. Published Print: JAN 2003


This unit illustrates how to use MEME to discover motifs in a group of related nucleotide or peptide sequences. A MEME motif is a sequence pattern that occurs repeatedly in one or more sequences in the input group. MEME can be used to discover novel patterns because it bases its discoveries only on the input sequences, not on any prior knowledge (such as databases of known motifs). The input to MEME is a set of unaligned sequences of the same type (peptide or nucleotide). 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. MEME also produces block diagrams showing where all of the discovered motifs occur in the training set sequences. MEME's hypertext (HTML) output also contains buttons that allow for the convenient use of the motifs in other searches.