GEM specifications

Information


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.
Input format BED+FASTA,SAM+FASTA
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

Subtools


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

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Versioning


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Documentation


Maintainers


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

Additional information


http://groups.csail.mit.edu/cgs/onePageGPS/ http://groups.csail.mit.edu/cgs/gem/

Publications for Genome wide Event finding and Motif discovery

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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