CompariMotif @ Bioware

CompariMotif takes two lists of regular expression protein (or DNA) motifs and compares them to each other, identifying which motifs have some degree of overlap. CompariMotif outputs a table of all pairs of matching motifs, along with their degree of similarity (information content) and their relationship to each other.

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Input options

Please enter Motifs here.
(Load example|Clear field)

Or select a file :

Please choose a comparison motif database here.
(Load example|Clear fields)

Or select a file :

Or select a database in the list :

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Normalised IC cut-off

Must exactly match all fixed positions
in the motifs from
Input motifs
Searchdb motifs
Boths input and searchdb motifs
Min. motif IC
Min. defined positions
Mismatches allowed

Trims Xs
Reverse motifs
Ambiguity Overlaps

For larger datasets please download standalone version here


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The CompariMotif webserver is currently powered by CompariMotif 3.11.

The legacy version of the Server is available here



Please cite :

When using results obtained with one of the motif databases provided, please cite the appropriate reference. (Click here for details.)

News and Updates

  • September 2013: upgraded to used REST API and CompariMotif 3.11, which recognises "Ugly" partially overlapping degenerate position matches that can be screened out with overlaps=F.
  • August 2012: upgraded to CompariMotif 3.6, which now accepts ELM downloads and variable-length non-wildcards (although these will be split).
  • August 2012: migration to new server. (Please report any odd behaviour.)
  • April 2012: new ELM database entries added.