About Glimmer

Glimmer is a system for finding genes in microbial DNA, especially the genomes of bacteria, archaea, and viruses. Glimmer (Gene Locator and Interpolated Markov ModelER) uses interpolated Markov models (IMMs) to identify the coding regions and distinguish them from noncoding DNA. The IMM approach is described in our original Nucleic Acids Research paper on Glimmer 1.0 and in our subsequent paper on Glimmer 2.0. The IMM is a combination of Markov models from 1st through 8th-order, where the order used is determined by the amount of data available to train the model. In addition, the positions used as context for the model need not immediately precede the predicted postion but are determined by a decision procedure based on the predictive power of each position in the training data set (which we term an Interpolated Context Model or ICM). The models for coding sequence are 3-periodic nonhomogenous Markov models. Improvements made in version 3 of Glimmer are described in the third Glimmer paper.

Glimmer was the primary microbial gene finder used at The Institute for Genomic Research (TIGR), where it was first developed, and has been used to annotate the genomes of thousands of bacterial, archaeal, and viral genomes around the world.

Versions

Glimmer version 3.02b is the current version of the system.

Glimmer has been pre-compiled for the Sun SPARC and Sun 64-bit (AMD) platforms by Mithun Sridharan. 

The previous, legacy version of Glimmer, v2.13, can still be downloaded by clicking here and is described on this page, including a summary of the changes made from Glimmer2 to Glimmer3.

Systems Related to Glimmer

For the eukaryotic version of Glimmer go to the GlimmerHMM site.

For the metagenomic version of Glimmer go to the Glimmer-MG site on github.

Both these systems are entirely separate programs from Glimmer, but both use Glimmer-style IMMs to distinguish coding from non-coding DNA.

Obtaining Glimmer

Glimmer is OSI Certified Open Source Software .

Click here to download the complete Glimmer3 system . After downloading, uncompress the distribution file by typing:

% tar xzf glimmer302b.tar.gz

A directory named glimmer3.02 will be created, containing a file glim302notes.pdf with instructions on compiling and running the system.

References

For descriptions of the three major versions of Glimmer see our papers:

• S. Salzberg, A. Delcher, S. Kasif, and O. White. Microbial gene identification using interpolated Markov models, Nucleic Acids Research 26:2 (1998), 544-548.
• A.L. Delcher, D. Harmon, S. Kasif, O. White, and S.L. Salzberg. Improved microbial gene identification with GLIMMER, Nucleic Acids Research 27:23 (1999), 4636-4641.
• A.L. Delcher, K.A. Bratke, E.C. Powers, and S.L. Salzberg. Identifying bacterial genes and endosymbiont DNA with Glimmer, Bioinformatics 23:6 (2007), 673-679.

Acknowledgements

Glimmer was supported in the past by the National Library of Medicine at NIH under grants R01-LM007938 and R01-LM06845 (to Steven Salzberg) and by the the National Science Foundation under grants IRI-9530462 and IIS-9902923 (to Steven Salzberg and Art Delcher). Currently it is supported by the National Institute of General Medical Sciences (NIGMS) at NIH under grant R01-GM083873.