Logo MotifLocator

MotifLocator calculates for each possible instance in a DNA sequence set how well it fits a given motif model (PWM) versus the genome-specific background model. A threshold cutoff on the background corrected PWM based score computed for each instance determines whether an instance in the sequence dataset is a motif or not.

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.

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 MotifLocater:

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 MotifLocator Guidelines) and overwrite whenever needed. Pressing Submit will initiate the MotifLocator 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.
  -f <filename>:   file with a list of sequences in Fasta format (EvgA example).
  -m <filename>:   file with the prior motif(s) in PWM format (EvgA example).
        please choose your way :
   
   
  -b <filename>:  file with the genome-specific background model in format (EvgA example),
        please choose your way :
   
   

  Output:
  -o <file>:   file with solutions in annotated instances format (EvgA example)

  Parameters:
  -s <0|1>:   default <1> both strands of the sequences will be analyzed (i.e. input sequences and the reverse complement).
      <0> is only input sequences.
  -t <value>:   threshold above which a motif instance is selected. Default <0.85>.
  -a <0|1>:   type of motif instance score reported. Default <0> reports the rescaled instance score that was evaluated against the threshold (-t). Option <1> reports the absolute instance score that reflects the likelihood that the instance belongs to the motif instead of the background.
  -l <filename>:   file listing prior motif identifiers to select from -m file. Default not used. (EvgA example)