The meaning of MEME E-values and p-values.

[CharlesEGrant]

MEME reports (an estimate) of the statistical significance of each motif it finds (the "motif E-value") as well as an estimate of how well each occurrence ("site p-value") matches the motif. The motif E-value is a fairly conservative estimate of how likely it is that the motif is not just a statistical artifact. The site p-values are not conservative, and should only be used as relative indications of how well each site matches the motif--they cannot be used to tell if the motif is "real" or not. The E-Value is reported in the summary for each motif, and is further described in the "Motifs" sub-section of "Explanation of MEME Results" in the MEME output. 

MEME uses an algorithm called Expectation Maximization to find short patterns of nucleic acids or amino acids that occur more frequently in the input sequences than would be expected by chance. Because these patterns need not be exact matches, they are described using a matrix: the Position Specific Scoring Matrix (PSSM). Once MEME has generated the PSSM, it uses a second algorithm, MAST, to find the best matches to that PSSM in the input data. The p-value tells you how well a particular site matches the PSSM found by MEME. The smaller the p-value, the more significant the match. 

The site p-value is described in the "Sites" sub-section of "Explanation of MEME Results" in the MEME output.