GEM (Genome wide Event finding and Motif discovery) is a software tool to study protein-DNA interaction using ChIP-Seq/ChIP-exo data. GEM resolves ChIP data into explanatory motifs and binding events at unsurpassed spatial resolution by linking binding event discovery and motif discovery with positional priors in the context of a generative model of ChIP data and genome sequence.
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Yuchun Guo, Georgios Papachristoudis, Robert C Altshuler, Georg K Gerber, Tommi S Jaakkola, David K Gifford & Shaun Mahony,
Discovering homotypic binding events at high spatial resolution.
Bioinformatics. 2010 Dec 15;26(24):3028-34. Epub 2010 Oct 21. PMID: 20966006.