ChIPMunk DNA&RNA motif discovery tool now comes in a single package with diChIPMunk, ready to process your ChIP-Seq, HT-SELEX, DNase footprints & similar data, including sequence data on RNA-binding proteins (e.g. PAR-CLIP or CLIP-Seq).

Our sequence-crunching rodents are now accompanied by SPRY-SARUS motif scanner, to apply discovered PWMs to look for motif hits in given sequence sets.

You may also check MACRO-APE and PERFECTOS-APE web tools, which are also useful for downstream analysis involving ChIPMunk results.

[NEW] Web-interface for ChIPMunk and diChIPMunk

ChIPMunk downloads

chipmunk.jar ChIPMunk v7 complied classes

userguide.pdf ChIPMunk v7 detailed user guide

Additional downloads

chipmunk_src.jar ChIPMunk v7 java sources ChIPMunk peak fasta examples ChIPMunk supporting scripts (ruby)

Please, use the latest versions provided at this page.

Citing ChIPMunk

Deep and wide digging for binding motifs in ChIP-Seq data. Kulakovskiy et al., 2010, PubMed

From binding motifs in ChIP-Seq data to improved models of transcription factor binding sites. Kulakovskiy et al., 2013, PubMed

Application of experimentally verified transcription factor binding sites models for computational analysis of ChIP-Seq data. Levitsky et al., 2014, PubMed


In case of any questions don't hesitate to contact [ivan-dot-kulakovskiy-at-gmail-dot-com].

This software is maintained by Ilya Vorontsov and Ivan Kulakovskiy.

SPRY-SARUS motif scanner

SPRy-SARUS stands for Straightforward yet Powerful Rapid SuperAlphabet Representation Utilized for motif Search. This simple tool uses superalphabet approach to scan a given set of sequences for (di)PWM hits scoring no less than a given threshold.

sarus.jar compiled classes   sarus_src.jar java sources example data   sarus_readme.txt short readme