About Glimmer-MG

Glimmer-MG is a system for finding genes in environmental shotgun DNA sequences. Glimmer-MG (Gene Locator and Interpolated Markov ModelER - MetaGenomics) uses interpolated Markov models (IMMs) to identify the coding regions and distinguish them from noncoding DNA. The IMM approach, described in our Nucleic Acids Research paper on Glimmer 1.0 and in our subsequent paper on Glimmer 2.0 , uses a combination of Markov models from 1st through 8th-order, weighting each model according to its predictive power. Glimmer uses 3-periodic nonhomogenous Markov models in its IMMs.

Glimmer-MG addresses the challenges of metagenomics gene prediction. Prediction model training is the main reason Glimmer3 cannot be applied to metagenomics sequences. Rather than rely on GC% to find evolutionary relative genomes for training, Glimmer-MG instead finds phylogenetic classifications using Phymm and parameterizes gene prediction models using those classifications. Glimmer-MG also clusters the sequences using Scimm, which groups together sequences that are likely from the same organism. Analogous to iterative schemes that are useful for whole genomes, Glimmer-MG retrains prediction models within each cluster on the initial gene predictions before making a final set of predictions. To account for fragmented genes, Glimmer-MG incorporates a model for gene length, in which partial genes are carefully handled. Finally, Glimmer-MG can predict insertions and deletions in the sequence by branching into a different frame at low quality base calls such as homopolymer runs in 454 sequences.

Send questions and help requests to David Kelley - dkelley [at] fas [dot] harvard [dot] edu.


Mar. 16, 2014 - Release 0.3.2
Installation fix.

Nov. 15, 2012 - Release 0.3.1
Phymm installation fix.

May 23, 2012 - Release 0.3
Minor bug fixes and a bug fix that kept g3-iterated.py from working properly.

Jan. 4, 2012 - Release 0.2
Fixed a problematic bug for retraining and some other smaller issues with installation and for very small clusters.

Jun. 1, 2011 - Release 0.1
Initial release!

Current Version

Manual        Download Glimmer-MG v0.3.2

This software is OSI Certified Open Source Software.


Manuscript Data

sim_data.tgz (2.1 Gb)



Glimmer is currently supported by the National Library of Medicine at NIH under grant R01-LM007938. It was previously supported by the National Science Foundation under grants IRI-9530462 and IIS-9902923, and by the National Institutes of Health under grant R01-LM06845.