We, Russian scientists of the autosome team, are depressed by the dire events caused by Russian military actions in Ukraine.
We express our condolences to all affected people and sincerely hope for a prompt transition to peace.

ChIPMunk: fast and efficient motif discovery tool

ChIPMunk is fast heuristic motif discovery tool for analysis of high-throughput sequencing data.

ChIPMunk utilizes both classic mononucleotide and advanced dinucleotide position weight matrices (diChIPMunk) to process your ChIP-Seq, HT-SELEX, DNase footprints & similar data. Motif discovery for RNA-binding proteins (single-stranded search) is also supported.

ChIPMunk identifies the strong motif with the maximum Kullback Discrete Information Content in a given set of nucletide sequences. ChIPMunk uses extended multifasta as the input format.

Web interface

Please cite:

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

Standalone command-line version (requires Java 1.6) and manual are available for download at ChIPMunk homepage.

Supported by RFBR grants 15-34-20423 and 16-34-01318.