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).

You can try ChIPMunk online using web-interface.

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.

Need a demo? Try online web-interface for ChIPMunk and diChIPMunk. Need a simple motif scanner? Try the newest SARUS.

ChIPMunk downloads

chipmunk.jar ChIPMunk latest (v8) complied classes

userguide.pdf ChIPMunk detailed user guide

Additional downloads

chipmunk_v8_src.jar ChIPMunk v8 java sources

chipmunk_v8.jar ChIPMunk stable (v8, currently the same as above) compiled classes 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

The newest update supporting bed output and P-values scoring is available at github. The classic version is provided below.

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