GEM- Genome wide Event finding and Motif discovery

GEM 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.

GEM has following features

Exceptionally high spatial resolution on binding prediction

Highly accurate de novo motif discovery

Resolve closely spaced (less than 500bp) homotypic events that appear as a single cluster of reads

Enable analysis of spatial binding constraints of multiple transcription factors, for detected TF dimer binding sites, enhanceosomes, etc.

Java 1.6 is required to execute the JAR. For analysis with mamalian genome, GEM requires about 5-15G memory. It can be specified at the command line with the option -Xmx (i.e. java -jar -Xmx10G gem.jar allocates 10GB of memory).

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