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.
chipmunk.jar ChIPMunk latest (v8) complied classes
userguide.pdf ChIPMunk detailed user guide
chipmunk_v8_src.jar ChIPMunk v8 java sources
chipmunk_v8.jar ChIPMunk stable (v8, currently the same as above) compiled classes
chipmunk_peaksample.zip ChIPMunk peak fasta examples
chipmunk_scripts.zip ChIPMunk supporting scripts (ruby)Please, use the latest versions provided at this page.
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.