Scan result mockup

Welcome to the CiiiDER home page

CiiiDER is a user-friendly tool for predicting and analysing transcription factor binding sites, designed with biologists in mind. CiiiDER can predict potential transcription factor binding sites within sequences, identify those transcription factors that are significantly enriched and display the results interactively.

The manuscript is available from PLOS ONE.

Scan result mockup

Scan results

CiiiDER can retrieve promoter sequences from a gene list or use FASTA format sequences and scan for transcription factor binding sites using supplied position frequency matrices. The results will be displayed as interactive map of predicted sites.

Enrichment plot output

Enrichment results

CiiiDER can then perform an enrichment analysis, comparing the frequency of transcription factor binding sites predicted in the input sequences to the frequency within a background set of sequences. These results will be displayed on the interactive binding site map, but will also be visualised as an interactive Plotly scatter plot.


Please visit the downloads page to try CiiiDER today.

Get in touch

Please contact us with any questions or suggestions.