GEM statistics

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GEM specifications


Unique identifier OMICS_00441
Name GEM
Alternative names Genome wide Event finding and Motif discovery, GPS (Genome Positioning System)
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data An alignment file of ChIP-seq reads and a genome sequence.
Output data A list of predicted binding events and the explanatory binding motifs and an optionnal files for load GEM results to Genome Browser as custom tracks for visualization.
Output format TXT/BED
Operating system Unix/Linux
Programming languages Java, Perl
Computer skills Advanced
Version 3.0
Stability Stable
Maintained Yes


  • KMAC (K-Mer Alignment and Clustering)
  • KSM (K-mer Set Memory)
  • RMD (Regulatory Module Discovery)



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  • person_outline David Gifford <>
  • person_outline Shaun Mahony <>

Additional information

Publications for Genome wide Event finding and Motif discovery

GEM in publications

PMCID: 4992276
PMID: 27544903
DOI: 10.1186/s12864-016-3006-6

[…] enrichment would correspond at times 2 and/or 5 min after stress) [, ]. our selection was further confirmed with two standard peak-calling methods, model-based analysis for chip-seq (macs) [] and genome wide event finding and motif discovery (gem) []. macs uses a poisson test to rank their candidate peaks and is considered one of the methods with higher sensitivity, while gem uses binomial […]

PMCID: 5429005
PMID: 27169896
DOI: 10.1093/bib/bbw035

[…] each of them in terms of how they solve sub-problems 1 and 2 ( and ). we chose model-based analysis for chip-seq version 2 (macs2) [], multiscale enrichment calling for chip-seq (music) [], genome wide event finding and motif discovery (gem) [], zero-inflated negative binomial algorithm (zinba) [], bayesian change point (bcp) [] and tm for further analysis to balance the need to cover […]

PMCID: 4526313
PMID: 26192440
DOI: 10.1038/ncb3210

[…] mouse genome (grcm37/mm9) with bowtie2 aligner (version 2.2.1). only the reads uniquely mapped to the genome were utilized for further analysis. e2f3 and myc dna binding peaks were identified using genome wide event finding and motif discovery algorithm gem (version 2.4.1) with a false discovery rate (fdr) less than 1% and model-based analysis of chip-seq algorithm macs2 (version 2.0.10) […]

PMCID: 4172970
PMID: 25204769
DOI: 10.1038/ncomms5868

[…] then generated using samtools version 0.1.18 (the sequence alignment/map format and samtools) and further sorted following chromosome order by picard version 1.100 ( genome wide event finding and motif discovery (gem) version 2.41 was used to detect the positive peak and motif discovery. default parameters were used, except—k_min was set to 5, -- k_max was set […]

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GEM institution(s)
Computational and Systems Biology Program, Massachusetts Institute of Technology, Cambridge, MA, USA
GEM funding source(s)
Supported by National Institutes of Health grant P01 NS055923.

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