Output format

The output is provided to the user via e-mail. It consists of 3 files:

• MMF-XXXX-clusters.txt - a text file containing clusters of motifs. For each of the clusters, the PWM of the consensus motif is reported.
• MMF-XXXX-newick.txt - a tree (in the Newick format) containing the tree obtained during hierarchical clustering of all motifs.
• MMF-XXXX-raw.txt - the file containing the raw output of all motif discovery programs selected by the user.

In all these files, the motifs are described by identifiers in the following form:

XXXXXXXXXX_YY_N

XXXXXX represents the consensus sequence of the motif, YY is an abbreviated name of the program which reported this motif, and N corresponds to the ranking of the motif given by the respective method.

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Abbreviated application names:

• bi: BioProspector
• me: MEME
• md: MDScan
• we: Weeder

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