ChIPMunk motif discovery tool now comes in a single package with diChIPMunk, ready to process your ChIP-Seq, HT-SELEX, DNase footprints & similar data.

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 v6d complied classes

userguide.pdf ChIPMunk v6 detailed user guide

Additional downloads

chipmunk_src.jar ChIPMunk v6d java sources ChIPMunk peak fasta examples ChIPMunk supporting scripts (ruby)

Please, always use the latest versions provided at this page: v6d fixes single-strand r: mode for diChIPMunk.

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