MotifRanking

MotifRanking reorganizes the solutions (PWMs) reported by multiple runs of MotifSampler (or another motif detector) on a given sequence set into in a shorter list of non-redundant motifs sorted by their likelihood score.

Reducing redundancy is obtained by grouping together solutions (PWMs) that represent the same motif, allowing at the same time to count the detection frequency of a candidate motif (also called return ratio RR). Each group is represented in the output of MotifRanking by the solution with the highest motif score (default the LogLikelihood score reported by MotifSampler) within the group. The motif with the highest motif score amongst the candidate motifs reported by MotifRanking that also has a minimal detection frequency (RR), represents the strongest and most likely overrepresented motif signal detected by MotifSampler in the given sequence set.

To optimally run this tool and evaluate its output, please consult our guidelines (includes link to a case study).
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.

Publications:

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

References :
- G. Thijs, K. Marchal, M. Lescot, S. Rombauts, B. De Moor, P. Rouze and Y. Moreau. A Gibbs Sampling method to detect over-represented motifs in the upstream regions of co-expressed genes. 2002. Journal of Computational Biology, 9 (3):447-464.
- G. Thijs, Y. Moreau, F. De Smet, J. Mathys, M. Lescot, S. Rombauts, P. Rouze B. De Moor, and K. Marchal. INCLUSive: INtegrated Clustering, Upstream sequence retrieval and motif Sampling. 2002. Bioinformatics, 18(2):331-2.

Run MotifRanking:

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 MotifRanking Guidelines) and overwrite whenever needed. Pressing Submit will initiate the MotifRanking software on our server. An url containing the results will be sent by email.
Illustrative examples are the result of running MotifSuite on an E. coli sequence set containing the known EvgA motif (as derived from RegulonDB)(read more on the benchmark data in the case study).