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Genome wide Event finding and Motif discovery GEM

Alternative name: GPS (Genome Positioning System)

Allows investigation of protein-DNA interaction by ChIP-Seq/ChIP-exo data. GEM is based on an integrative computational method and intends to provide both improved spatial accuracy of binding event predictions and improved motif discovery in ChIP-Seq and ChIP-exo datasets. It has been selected to be part of the ENCODE TF ChIP-seq analysis pipeline.

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GEM classification

GEM specifications

Software type:
Application/Script
Restrictions to use:
None
Input format:
BED+FASTA,SAM+FASTA
Output format:
TXT/BED
Programming languages:
Java, Perl
Version:
3.0
Maintained:
Yes
Interface:
Command line interface
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.
Operating system:
Unix/Linux
Computer skills:
Advanced
Stability:
Stable

GEM distribution

versioning

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No versioning.

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GEM support

Documentation

Maintainers

  • David Gifford <>
  • Shaun Mahony <>

Additional information

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

Credits

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Publications

Institution(s)

Computational and Systems Biology Program, Massachusetts Institute of Technology, Cambridge, MA, USA

Funding source(s)

Supported by National Institutes of Health grant P01 NS055923.

Link to literature

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