MEME (Multiple Em for Motiv Elicitation) 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 and outputs as many motifs as requested. MEME uses statistical modeling techniques to automatically choose the best width, number of occurrences, and description for each motif.
MCAST searches sequences for clusters of matches to one or more nucleotide motifs
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MCAST: Scanning for cis-regulatory motif clusters.
Grant CE, Johnson J, Bailey TL, Noble WS.
Bioinformatics. 2015 Dec 24. pii: btv750
The MEME Suite.
Bailey TL, Johnson J, Grant CE, Noble WS.
Nucleic Acids Res. 2015 May 7. pii: gkv416.
Timothy L. Bailey, Mikael Bodén, Fabian A. Buske, Martin Frith, Charles E. Grant, Luca Clementi, Jingyuan Ren, Wilfred W. Li, William S. Noble,
“MEME SUITE: tools for motif discovery and searching“,
Nucleic Acids Research, 37:W202-W208, 2009