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CompariMotif Options
For a full list of options, please see the CompariMotif Manual.
In addition to the Input options, the following basic options are available:
Basic options. The right-hand column indicates the commandline equivalent for each webserver option.
| Server Option
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Description
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Commandline Option
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| Normalised IC cut-off |
The minimum normalise IC allowed for a match. |
normcut=X |
| Must exactly match all fixed positions |
By default, fixed positions of one motif may match degenerate positions of another.
This option allows the user to restrict matches to those where any fixed positions in either, neither or both motifs
must match a corresponding fixed position in the other motif. This can be useful, for example, for tyrosine
phosphorylation motifs where the fixed tyrosine must be present and cannot match anything else. |
matchfix=X |
Clicking on Motif Filtering & Advanced Options should present the additional options listed in the table, below:
Advanced options. The right-hand column indicates the commandline equivalent for each webserver option.
| Server Option
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Description
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Commandline Option
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| Min. motif IC |
Minimum information content (IC) of motifs. Motifs a lower IC will be excluded from the comparison.
IC is scaled from 0.0 for a wildcard position to 1.0 for a fixed position. |
minic=X |
| Min. defined positions |
Minimum number of defined (non-wildcard) positions. Motifs with fewer defined positions will be excluded from the comparison. |
minpep=X |
| Mismatches allowed |
The number of mismatched positions to be tolerated between two motifs. |
mismatches=X |
| Trim Xs |
Whether to trim leading and trailing wildcards. These will not contribute to motif scoring but will affect the match/parent/subsequence/overlap
relationships (see CompariMotif Relationships). |
mismatches=X |
| Reverse motifs |
Reverses the input motifs. If you get a lot of CompariMotif hits, this option can give a
sense of how many hits to expect giving the amino acid composition of your motifs and the CompariMotif settings selected. |
reverse=T/F |
| DNA |
Whether motifs should be considered as DNA motifs. |
dna=T/F |
| AA Freq. File |
Replace uniform AA Frequencies with those from a file (can be fasta file of sequences or
delimited frequency file). |
aafreq=FILE |
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