Welcome to MotifScan Web Toolkit


Scan input genomic regions with known DNA motifs

Given a set of input genomic regions, MotifScan scans the sequences to detect the occurrences of known motifs. It can also applies a statistical test on each motif to check whether the motif is significantly over- or under-represented (enriched or depleted) in the input genomic regions compared to another set of control regions.


motifscan workflow

This web toolkit is a user-friendly interface based on the scan command of the command-line version of MotifScan.

How to use

You may download sample input here or check out sample outputs here. To use the sample input, please upload it as the region file and select "hg19" for the genome name.

  1. Go to the input page.
  2. Specify the genomic regions to be scanned and the genome name.
  3. Set desired parameters. Default values are pre-populated. Explanations are shown in the info boxes.
  4. For the control file, 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 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.