Welcome to MAmotif Web Toolkit


MAmotif is used to compare two ChIP-seq samples of the same protein from different cell types or conditions (e.g. Mutant vs Wild-type) and identify transcriptional factors (TFs) associated with the cell-type biased binding of this protein as its co-factors, by using TF binding information obtained from motif analysis (or from other ChIP-seq data).

MAmotif automatically combines MAnorm model to perform quantitative comparison on given ChIP-seq samples together with Motif-Scan toolkit to scan ChIP-seq peaks for TF binding motifs, and uses a systematic integrative analysis to search for TFs whose binding sites are significantly associated with the cell-type biased peaks between two ChIP-seq samples.

When applying to ChIP-seq data of histone marks of regulatory elements (such as H3K4me3 for active promoters and H3K9/27ac for active promoter/enhancers), or DNase/ATAC-seq data, MAmotif can be used to detect cell-type specific regulators.

Note: To use MAnorm independently, please visit our site for MAnorm Web Toolkit.

This web toolkit is a user-friendly interface based on the command-line version of MAmotif and used to run complete MAmotif workflow.

How to use

You may download sample inputs here or check out sample outputs here. To use the sample inputs, please select "hg19" as the genome name.

  1. Go to the input page.
  2. Select files for peaks and reads for the two samples.
  3. Set desired parameters. Default values are pre-populated. Explanations are shown in the info boxes.
  4. Make sure you select the matched file formats.
  5. Click the "analyze" button to run. Please be patient as uploading files may take some time.

You will receive a link to the page that will later display your results and allow you to download all the output data as a zip file.

Note: Due to the uncertainty of computation workload, the waiting time is not garuanteed.


mamotif workflow