Frequently Asked Questions
- Q. Why don't the motif occurrences in the "Summary of
Motifs" block diagrams match the occurrences shown in the
individual motif block diagrams?
A. This is a feature, not a bug. The motif occurrences shown for a motif in its section of the output are the ones discovered by the MEME algorithm. These occurrences are then used to create a position specific scoring matrix (PSSM) for the motif. The PSSMs for all of the motifs discovered by MEME are then used to search for non-overlapping sets of occurrences of motifs with p-values under 0.0001 using the MAST algorithm. These are displayed in the "Summary of Motifs" block diagram. Individual motif occurrences will sometimes be missing from the "Summary of Motifs" block diagram because of the non-overlapping or minimum p-value requirements. Conversely, there may be motif occurrences in the summary diagram that were not discovered by the MEME algorithm.
Click here for more information on MAST.
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