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CompariMotif Output
The main output of CompariMotif is a sortable text table with the fields given in the table below. Clicking on a field header will sort the table on that field. This may be slow for large results tables. It is recommended these are downloaded for analysis in e.g. MS Excel. It is recommended that results are ranked by Score. This is a heuristic but matches with higher scores generally seem to be of better quality.
In addition to the main results table, CompariMotif outputs an XGMML file that can be imported directly into Cytoscape for visualisation. The Manual gives more details on how to do this. See also the Example Application for an example of this visualisation for a real analysis.
Note. If CompariMotif is being run directly from the SLiMDisc webserver, the top 20 motifs returned by SLiMDisc will be compared to a local database consisting of ELM, MiniMotif and some additional SLiMs identified from the literature. Output is a table of top 20 SLiMDisc motifs and the known SLiMs they match with the chosen settings.
Main Output Table Fields
| Name1 | This will give the name of the SLiMDisc dataset (SLiMDisc_temp_X, where X is the job ID) followed by #R, where R is the rank of the motif that has hit a known SLiM. |
| Name2 | This is the name of the known SLiM that has been hit. This may be an ELM or MiniMotif ID. |
| Motif1 | The motif definition (pattern) of the SLiMDisc motif. |
| Motif2 | The motif definition (pattern) of the known SLiM. |
| Similarity1 | The relationship of the SLiMDisc motif to the known SLiM. (See CompariMotif Relationships.) |
| Similarity2 | The relationship of the known SLiM to the SLiMDisc motif. (See CompariMotif Relationships.) |
| Match | Regular expression of match between motifs. Upper case positions indicate an exact match, while lower case positions have some degree of degeneracy difference between the two motifs. Mismatches are marked with an asterisk. |
| MatchPos | The number of matching non-wildcard positions. (This includes positions that match due to ambiguities.) This must meet the minshare requirement. (See Options.) |
| MatchIC | The calculated information content of the match. (See the CompariMotif Manual for details.) |
| NormIC | The calculated information content of the match normalised by the maximum possible MatchIC for that pair of motifs. In essence, higher scores indicate better matches, and a score of 1.0 indicates that no better match was possible between this pair of motifs. (See the CompariMotif Manual for details.) |
| Score | This is a heuristic score (MatchIC x NormIC) for ranking motif matches. Although there is no absolute definition of what makes interesting motif match, matches with higher scores will tend to be of better quality. (See the CompariMotif Manual for details.) |
| Info1 | The information content of the SLiMDisc motif. (Scaled so that 1.0 is the equivalent of 1 fixed position, no gap penalty.) |
| Info2 | The information content of the known SLiM. (Scaled so that 1.0 is the equivalent of 1 fixed position, no gap penalty.) |
| Desc1 | The description of the SLiMDisc motif, which is the same as Name1. |
| Desc2 | The description of the known SLiM. |
Example Output
Example output produced for a search of SLiMFinder motifs vs. ELM, sorted by Score.
This output is produced if the example Input is searched against ELM with a Normalised IC cut-off of 0.4 and matches constrained such that fixed positions in the SearchDB (ELM) motifs must match fixed positions in the query motifs, as in the Example Application. See the Example Application or Manual for XGMML output.