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.
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.