# The MEME Suite

## Motif-based sequence analysis tools

## MoMo Output Formats

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- MoMo Results HTML Format

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- MoMo Results TSV Format

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- MoMo Results Text Format

### MoMo Results HTML Format

See this sample HTML results file.

The MoMo HTML file contains five sections:

- Links: links to 1) the first motif found, 2) debugging information, 3) the results in TSV format, and the motifs in MEME motif format
- Program Information: version, availability and citation information
- Peptide Preprocessing: information on MoMo's preprocessing of the modified peptides in its input
- Results: the motifs found by MoMo
- Debugging Information: the command line and the parameters given to MoMo

Motifs are reported in the Results section in the order in which they are found by MoMo. The entry for each motif contains three entries:

- Motif Description Line: the regular expression for the motif and various statistics
- Sequence Logo: a visual representation of the motif
- Motif Occurrences: the list of foreground peptides matching the motif

The Motif Description Line contains the following fields, depending on the algorithm you chose:

- All algorithms
  - 'motif:' - (a string similar to) a regular expression describing the motif. Lower case 'x' represents a match to any residue the non-central positions. The central peptide and its modification weight (if any) is surrounded by '_' characters. If --single-motif-per-mass was specified, the central peptide will be represented by an uppercase 'X', which also represents a match to any residue.
- simple
  - 'motif:' - the regular expression describing the motif. Lower case 'x' represents the wildcard character in the non-central positions. The central peptide and its modification weight (if any) is surrounded by '_' characters. If --single-motif-per-mass was specified, the central peptide will be represented by an uppercase 'X'.
  - 'fg_matches:' - the number of peptides matching the motif.
- motif-x or modl
  - 'score:' - the algorithm-dependent score. For motif-x, this is the sum over the significant position/residue pairs of -log(pbinomial); for modl, this is the increase in description length in bits if that motif was removed from the final set of motifs.
  - 'fg:' - the number of foreground peptides matching the motif, followed by '/', followed by the total number of foreground peptides with the given central modification.
  - 'bg:' - the number of background peptides matching the motif, followed by '/', followed by the total number of background peptides with the given central modification.
  - 'fg/bg:' - the fold enrichment of the foreground vs. the background counts.
  - 'unadjusted p-value:' - the p-value of the Fisher Exact test on the enrichment of the motif in the foreground vs. the background peptides. This value does NOT accurately represent the statistical significance of the motif, but should be interpreted as a score only.
- motif-x -- The following additional fields appear for motif-x when used without --db-background, and DO accurately represent the statistical significance of the motif.
  - 'tests:' - the number of independent tests performed in the search for the motif, which is the number of position/residue pairs motif-x tested for statistical significance.
  - 'adjusted p-value:' - the p-value of the Fisher Exact test on the enrichment of the motif in the foreground vs. the background peptides, adjusted for the number of independent tests (1 - (1-pvalue)^tests).
- Note 1: For motif-x, the foreground and background counts are based on all the peptides unless the --harvard option is specified, in which case the counts are based on the remaining peptides.

### MoMo Results TSV Format

See this sample TSV results file.

The Results TSV file contains the same information as the Motif Description Line (see above) in the HTML output format. The column headers are self-explanatory.

### MoMo Results Text Format

See this sample motifs file.

The Results Text file contains each of the motifs found by MoMo in MEME motif format. MoMo creates these position-frequency matrix motifs by aligning the foreground peptides matching the motif and computing the position-frequency matrix. No pseudo-counts are added. For motif-x motifs, MoMo writes the value of 'tests' times the 'unadjusted p-value' in the E-value field, and '1' in that field for all other types of motifs.