The MEME Suite

Various MEME Suite programs (including MEME) construct a consensus sequence to be used as a name for a motif. The consensus sequence provides a convenient way to refer to the motif, but is not intended to be used as a replacement for the motif for searching for matches in sequences or other purposes. You should use the actual motif (PSPM or PSSM representation contained in the MEME Motif Format) for those purposes.

Note: DREME motif names are regular expressions, not consensus sequences, and are not constructed in this way.

A consensus sequence is constructed from each column in a motif's frequency matrix using the "50% rule" as follows.

1. The letter frequencies in the column are sorted in decreasing order.
2. Letters with frequency less 50% of the maximum are discarded.
3. The letter used in this position in the consensus sequence is determined by the first rule below that applies:
• If there is only one letter left, or if the remaining letters exactly match an ambiguous symbol in the alphabet, the letter or ambiguous symbol, respectively, is used.
• Otherwise, if the remaining set contains at least 50% of the core symbols in the alphabet, the alphabet's wildcard (e.g., "N" for DNA or RNA, and "X" for protein) is used.
• Otherwise, the letter with the maximum frequency is used.