Logo MotifComparison

MotifComparison analyzes whether your motif (the query motif) corresponds to any of previously described motifs reported in curated databases or detected by yourself in previous analyses. The algorithm computes a similarity metric between the compared PWMs and uses a threshold cutoff to decide upon similarity of the respective motifs.

To optimally run this tool and evaluate its output, please consult our guidelines.
Stand-alone executable: download.

The speed with which results are generated depends on the server load.

Last software revision : . (updated April 21, 2020)

Questions & suggestions: contact us.

References :

If you like our software, please use the MotifSuite publication for citing : MotifSuite publication.

References :
- reference on BLiC : Habib N, Kaplan T, Margalit H, Friedman N. A Novel Bayesian DNA Motif Comparison Method for Clustering and Retrieval. 2008. PLoS Comput Biol 4(2): e1000010. doi:10.1371/journal.pcbi.1000010.

- reference on motif databases : Source Release Numbers and Citation


Run MotifComparison:

To run this application, please fill in the required input in the blank fields. In the output section, a (randomized) file name has been generated. You can overwrite this automatically generated filename with a more meaningful description if desired (do not use spaces, dots, colons,... in this name). The program parameters have been set to a default value. Please analyze if these settings apply to your case (checkout our MotifComparison Guidelines) and overwrite whenever needed. Pressing Submit will initiate the MotifComparison software on our server. An url containing the results will be sent by email.
  Input:
  Your email address,   we will mail you the url with the result.
  -m <filename>  : file with query motifs in PWM format (EvgA example)
  -d <filename>  : file with database motifs in PWM format, please choose your way :
 
 

  Ouput:
  -o <file>:   file with similarities between the query motif and each database motif.
    Only non-## lines are similar motifs !   (EvgA_KL example, EvgA_pBLiC example)
    Choose your output format :

  Parameters:
  -l <0|1>:   similarity metric used when comparing two PWMs. Default <0> is Kullback-Leiber distance (KL), <1> is p-value of Bayesian Likelihood 2-Component score (p-BLiC).
  -x <value>:   minimum required overlap between two PWMs being compared. Default <6>.
  -s <value>:   maximal allowed shift between two PWMs being compared. Default <1>.
  -t <value>:   threshold below which two motifs are judged to be similar.
    Default KL <0.4>, default p-value BLiC <0.001>.