GEM
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Application data |
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| Created by | Yuchun Guo, Shaun Mahony & David K Gifford |
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| Biological application domain(s) | ChIP-seq |
| Principal bioinformatics method(s) | Peak calling, Sequence motif discovery |
| Technology | Illumina HiSeq, Illumina Solexa |
| Created at | Massachusetts Institute of Technology (MIT) |
| Maintained? | Yes |
| Input format(s) | BED, SAM, BAM, Bowtie, ELAND |
| Software features | probabilistic mixture model, motif prior, multi-threading |
| Programming language(s) | Java |
| Licence | Commercial, Freeware |
| Operating system(s) | Cross-Platform |
Summary: GEM is a java software tool to analyze transcription factor binding ChIP-seq/ChIP-exo data. It predicts binding events, performs de novo motif discovery and use the motif to improve the binding event calling. It calls binding events right at (or very close to ) the motif positions, deconvolves closely spaced homotypic binding events and accurately discovers binding motifs.
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Description
GEM is a software tool to study protein-DNA interaction using ChIP-seq/ChIP-exo data. GEM links binding event discovery and motif discovery with positional priors in the context of a generative probabilistic model of ChIP data and genome sequence, resolves ChIP data into explanatory motifs and binding events at unsurpassed spatial resolution .
GEM has following features:
- Exceptionally high spatial resolution on binding event prediction (aka peak calling)
- 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 detecting TF dimer binding sites, enhanceosomes, etc.
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