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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 100s of bacterial and archaeal species from TIGR and other labs. Glimmer3 predictions are available for all NCBI RefSeq bacterial genomes at their ftp site.

Versions

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

Version 3.02 Release Notes        Download Glimmer v3.02

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.

A new version of Glimmer, Glimmer4, is in preparation and will be released soon. It will incorporate features from Glimmer-MG and will include support for using proteomics information in calling genes.

Glimmer on the Web

A Glimmer server is available on the NCBI website. To run Glimmer on your sequence, visit NCBI Glimmer

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.

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:

Acknowledgements

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.